UK Ontology Network (UKON) 2018 - Call for contributions

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UK Ontology Network (UKON) 2018  - http://ukontology.org/

The UK Ontology Network is a meeting now in its sixth year. Its aim is to enable the sharing of knowledge about ontologies, vocabularies and any other mechanisms for organising, searching and sharing of knowledge. 

We aim to encourage participation from many different sectors: academic, public and private. Therefore, we have a light-weight submission process, and do not ask for formal publications. The meeting itself is friendly and informal, with plenty of opportunities for networking.

This year, the meeting will be hosted by Keele University, Staffordshire, UK.

We invite contributions in all the relevant domains including, but not limited to:

• Geographic Information

• Social Media

• Traditional Media

• Health and Biology

• Finance

• Security

• Governmental Data

Applications may include, but not limited to:

• Knowledge graphs

• Ontology curation & annotation

• Data publishing

• Data integration

 We invite short abstracts for talks, demos and posters. The abstracts should be around 300 words. The main review criteria are the relevance and balance across the topics of interest to the UKON community. Please submit using the following link:

     https://easychair.org/conferences/?conf=ukon2018

In addition, if you want to display a poster during the poster session, please get in touch with the local organisers. 

Although this is a UK-centric network, we encourage participation from those in Europe and across the world.

A small registration fee (£35) will be charged to cover catering.

Deadline for submissions: 2nd March, 2018

Deadline for notifications: 16th March, 2018

Workshop day: 30th April, 2018 

 

UKON 2018 organisers

Dr Goksel Misirli & Dr Allison Gardner (Keele University)

Dr Phillip Lord & Dr Jennifer Warrender (Newcastle University)

Dr James Malone (FactBio) 

Prof. Robert Stevens (Manchester University)

 

The 14th Symposium on Integrative Bioinformatics IB2018

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14th International Symposium on Integrative Bioinformatics

13-15 June 2018, Rothamsted Research, Harpenden, UK

http://imbio.de/ib2018

The 14th Symposium on Integrative Bioinformatics will be of interest to bioinformaticians, computer scientists, computational and systems biologists, and others working or interested in the developing area of integrative bioinformatics. The meeting will provide an excellent environment and a range of opportunities to present and discuss methods, theoretical approaches, and their practical applications.

Topics of interest include, but are not limited to:

  • Big Data: Large-scale systems for text and graph analysis, biomedical knowledge discovery and data mining, optimization, tool integration and workflow systems, novel algorithmic and statistical techniques for big data.
  • Data Science: Methods for analysing biological data, networks, time series; mining sequences, omics data, protein structures and functions, gene regulatory networks, genotype to phenotype data.
  • Foundations: Databases and data warehouses, biological ontologies, linked data; models and algorithms; machine learning; classification, clustering, regression; visualization.

 Paper submissions:

The IB Program Committee invites the submission of original papers describing innovative big biological data research, novel applications and technical contributions to all aspects of integrative bioinformatics. 

Deadline: *March 2, 2018*

All full paper submissions will be rigorously evaluated in a peer review process. Accepted papers will appear in the JIB special issue, Issue 3/3rd Quarter 2018, in the Journal of Integrative Bioinformatics (JIB) by de Gruyter. JIB is an open access journal publishing original peer-reviewed research articles in all aspects of integrative bioinformatics. JIB (ISSN 1613-4516) is indexed/tracked/covered by PubMed (since 2008), DBLP Computer Science Bibliography and Google Scholar.

By submitting a paper, the author(s) agree that, if their paper is accepted, they will: (1) Submit a final, camera-ready version to the publisher on or before the camera ready deadline. (2) Register at least one author to attend the conference on or before the registration deadline. (3) Attend the conference (at least one author). (4) Present the accepted paper at the conference.

Key dates:

  • March 2: Full Paper submission deadline
  • April 6: Notification of acceptance
  • April 20: Camera-ready deadline
  • April 20: Short talk abstract submission deadline
  • May 18: Poster abstract submission deadline

 

Local organizers:

Keywan Hassani-Pak, Rothamsted Research, UK

Chris Rawlings. Rothamsted Research, UK

Contact: IB2018@rothamsted.ac.uk

FAIRsharing

NIH Data Commons Pilot Phase to seek best practices for developing and managing a data commons.

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Professor Susanna-Assunta Sansone is co-Principal investigator in three of the twelve projects awarded prestigious USA National Institutes of Health (NIH) Data Commons funding, announced on the 6th November.

Over the next 4 years the awardees will work together, as the NIH Data Commons Pilot Phase Consortium (DCPPC), to accelerate new biomedical discoveries by making the digital products of biomedical research - such as data and tools - Findable, Accessible, Interoperable and Reusable for more researchers, according to the widely accepted FAIR principles.

"As an author of the FAIR principles, I am a strong promoter of a Data Science culture that considers the research, development and educational activities in and around digital research assets as science, rather than just a service" says Professor Sansone, Associate Professor and Associate Director at the Oxford e-Research Centre, part of the University of Oxford's Department of Engineering Science. "The NIH Data Commons will contribute to turn the concept of FAIR data into reality, and I am delighted to be at the forefront of these activities".

The awardees of the NIH DCPPC will pilot principles, metrics, policies, processes, and architectures needed to create the Data Commons, a shared virtual space where scientists can collaboratively access and share data and analytical tools. The work will be carried out using three high-value NIH biomedical datasets chosen based on their value to users in the biomedical research community, the diversity of the data they contain, and their coverage of both basic and clinical research: (i) Trans-Omics for Precision Medicine (TOPMed) Program; (ii) Genotype-Tissue Expression (GTEx) project; and (iii) Model organism databases (MODs).

"Harvesting the wealth of information in biomedical data will advance our understanding of human health and disease," says NIH Director Francis S. Collins, M.D., Ph.D. "However, poor data accessibility is a major barrier to translating data into understanding. The NIH Data Commons Pilot Phase is an important effort to remove that barrier."

Professor Sansone is already a co-Principal investigator in two NIH Big Data to Knowledge centres, funded during the first phase of this data science programme. "My team and I are thrilled to continue as part of this second phase of the programme, where we will also bring elements of our ISA and FAIRsharing resources, part of the ELIXIR-UK Node, and linked to the Research Data Alliance and Force11 communities. It is particularly significant to be the only co-Principal investigator involved in three projects, each led by renowned data scientists and colleagues, and the only UK university represented in the consortium", she says.

The three projects Professor Sansone's team will contribute to are the University of Maryland NIH Data Commons Facilitation Center; a Development and Implementation Plan for Community Supported FAIR Guidelines and Metrics; and Cloud Agnostic Architecture to locate Indexed FAIR objects and safely reuse them in new integrated analyses.

http://www.oerc.ox.ac.uk/news/NIH-award

ISA Tools used in NASA GeneLab data collection

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The open source ISA framework and tools, which help to manage an increasingly diverse set of life science, environmental and biomedical experiments (seeISAcommons), are being used by NASA for its GeneLab platform, which expands scientists' access to research carried out in space environments.

The ultimate goal of GeneLab is to enable space exploration by allowing researchers to understand the complex responses of biological systems to the space environment.

The vast amounts of raw omics data generated by experiments aboard the International Space Station will be made available to scientists and computational researchers worldwide in an open access database.

The GeneLab data repository hosts space biology and space-related datasets funded by multiple space agencies around the world. Study data hosted in the repository include a metadata definition file formatted according to the Investigation/Study/Assay (ISA) tab-delimited (tab) (ISA-Tab) specification, which can be produced using the ISA-tools ISACreator application with a customized GeneLab configuration.

The ISA model is a general-purpose model to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) mainly from 'omics-based' experiments employing a combination of technologies.

FAIRsharing

FAIRsharing

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Following community and adopter feedback, BioSharing.org has been re-branded to FAIRsharing.org. The new homepage is accessible at https://www.fairsharing.org. FAIRsharing will continue to refine and add to the content and functionality of the site over the summer to complete the transition. All links to BioSharing.org or to individual BioSharing records now redirect to the new site.

This re-branding reflects the broadened scope of the resource, to cover more types of standards, repositories and policies and to include more records, such as those for generic resources. The old BioSharing collection of resources will become a specific view on the biodomain, along with others that focus on other domains, such as agriculture, medicine, or environmental science.

As ELIXIR encompasses many life sciences domains (not just bio), it is essential to reflect the name in the context of the ELIXIR Interoperability Platform, and any presentations and leaflets.

Dr Ruth Bastow joins ELIXIR-UK as its Node Coordinator

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Ruth Bastow will take on the role of ELIXIR-UK Node Coordinator from August 2017. In doing so she will build on her great experience of network and consortium coordination. The Node Coordinator role is key for ensuring the smooth running of the Node including its interactions with the ELIXIR Hub and its community building within the UK.

Ruth was the Executive Director of Global Plant Council from 2013-2017. From 2004–2013 she worked as the Coordinator for the UK Arabidopsis Research Network, GARNet. In collaboration with colleagues Ruth established the UK Plant Sciences Federation (UKPSF) in 2009 and was awarded the Society of Biology President’s Medal for her support of the UK plant sciences community.

Before pursuing a career in science administration and policy Ruth worked as a postdoctoral researcher in the labs of Professor Caroline Dean (John Innes Centre) and Professor Julie Gray (University of Sheffield). She carried out her PhD in the lab of Professor Andrew Millar (University of Edinburgh).

Hands-on Introduction to HPC - Registration open

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This course provides an introduction to High-Performance Computing (HPC) for researchers in the life sciences, using ARCHER as a platform for hands-on training exercises.

Full detail & Registration:

http://bioexcel.eu/events/hands-on-introduction-to-hpc-for-life-scientists/

Overview

High-performance computing (HPC) is a fundamental technology used to solve a wide range of scientific research problems. Many important challenges in science such as protein folding, the search for the Higgs boson, drug discovery, and the development of nuclear fusion all depend on simulations, models and analyses run on HPC facilities to make progress.

This course introduces HPC to life science researchers, focusing on the aspects that are most important for those new to this technology to understand. It will help you judge how HPC can best benefit your research, and equip you to go on to successfully and efficiently make use of HPC facilities in future. The course will cover basic concepts in HPC hardware, software, user environments, filesystems, and programming models. It also provides an opportunity to gain hands-on practical experience and assistance using an HPC system (ARCHER, the UK national supercomputing service) through examples drawn from the life sciences, such as biomolecular simulation.

Learning outcomes

On completion of the course, we expect that attendees will understand and be able to explain:

• Why HPC? – What are the drivers and motivation? Who uses it and why?

• The UK & EU HPC landscape – HPC facilities available to researchers

• HPC hardware – Building blocks and architectures

• Parallel computing – Programming models and implementations

• Using HPC systems

• Access

• Batch schedulers & resource allocation

• Running jobs

• Dealing with errors

• Compiling code

• Using libraries

• Performance

• The Future of HPC

Pre-requisites

This course follows on naturally from the BioExcel Summer School on Foundation skills for HPC in computational biomolecular research (http://bioexcel.eu/events/bioexcel-summer-school/).

Familiarity with basic Linux commands (at the level of being able to navigate a file system) is recommended. You may find a Linux ‘cheat sheet’ such as http://www.archer.ac.uk/documentation/user-guide/linux.php#quickref useful if you are less familiar with Linux.

No programming skills or previous HPC experience is required.

Desktop computers running Windows will be available, however you are encouraged to bring your own laptop (running Windows, Linux, or macOS) as you will find it useful to learn how to set this up to connect to ARCHER (with assistance from course helpers if needed) and perform the hands-on practicals.

BioSchemas

Bioschemas Agreement meeting 24-26 May 2017

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The Bioschemas Implementation study organised its second meeting on May 24-26 at Hinxton. Bioschemas aims to improve data discoverability by encouraging the use of schema.org markup in websites and services. By using consistently structured information, the resources become more discoverable, facilitating collation and analysis of distributed data. Bioschemas is part of the wider schema community that is overseen by the schema.org consortium founded by Google, Microsoft, Yahoo and Yandex.

The implementation study supports three hackathons to specify, agree and adopt Bioschemas specifications in exemplar life sciences areas: data repositories, datasets, beacons, samples and phenotypes, and protein annotations. The second, agreement meeting had the aim of completing the definition of use cases and specifications, defining the relationship among the proposed data types, and publishing the first version of the proposed Bioschemas content types.

The next meeting will be held at Hinxton on October 2-4. It will have the aim of reporting on the experience of implementing the Bioschema specifications in exemplar services and refining them in light of these experiences.

More information about Bioschemas can be seen at www.bioschemas.org

Bioinformatics training courses at the University of Cambridge

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The following Bioinformatics Training events, taking place at the University of Cambridge, are currently open for booking. Although some of them are already fully booked, we encourage registering as you will be added to the waiting list and notified when a place becomes available.
  • Please note that these courses are only free for University of Cambridge students.All other participants will be charged a registration fee in some form.
  • It is the participant’s responsibility to acquire approval from their line manager/supervisor to attend any of these courses.
  • Please review full charging policy at the end of this email. 



2-3 May
Focuses on methods for the analysis of small non-coding RNA data obtained from high-throughput sequencing (HTS) applications (small RNA-seq). During the course, approaches to the investigation of all classes of small non-coding RNAs will be presented, in all organisms.
 
2 May
The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information.
 
4-5 May
Provides an introduction to the tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq data.


15-16 May
This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work.
 
15-16 May
Provides an introduction to the R programming language and software environment for statistical computing and graphics. A variety of examples with a biological theme will be presented.
 
17 May
Guides novice users through the process of analysing interaction networks – that allow biologists to map and characterise signalling pathways and to predict the function of unknown proteins.
 
18-19 May
Provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS). 


25-26 May
This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers using the REST API to query the core, variation, compara and functional genomics (regulation) databases.


12-13 June
Provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs.
 
14 June
Covers all aspects of the analysis of DNA methylation using sequencing, including primary analysis, mapping and quality control of BS-Seq data, common pitfalls and complications.
 
15-16 June
Provides an introduction to the R programming language and software environment for statistical computing and graphics. A variety of examples with a biological theme will be presented.

19-20 June
Provides an overview of metabolomics and its applications in life sciences, clinical and environmental settings.


21 June
This course will cover concepts and strategies for working more effectively with Python with the aim of writing reusable code.


22-23 June
Familiarizes the participants with the primary analysis of datasets generated through two popular high-throughput sequencing (HTS) assays: ChIP-seq and RNA-seq.
 
26-28 June
Focuses on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines.
 
10-11 July
Covers data resources and analytical approaches for the discovery and interpretation of bio-macromolecular structures.


12-14 July
Focuses on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.
 
All scheduled courses can be found at: http://training.csx.cam.ac.uk/bioinformatics/Event-timetable

Registration charges:
  • Free for University of Cambridge students.
  • £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level.
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from External Institutions and Charitable Organizations. These charges must be paid at registration.
  • £ 100/day for all Industry participants. These charges must be paid at registration.

Full details of our charging policy can be found at:http://training.csx.cam.ac.uk/bioinformatics/info/charging

Please note that it is the participant’s responsibility to acquire approval from their line manager/supervisor to attend any of these courses.

ELIXIR-UK awarded by BBSRC

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ELIXIR-UK has been awarded an International Partnering Award by BBSRC. The award, for £20,000 over 18 months from April 2017, will support networking activities (particularly travel) by Node members who need to travel to ELIXIR events but are currently not funded to do so. This will help UK partners become more integrated into ELIXIR activities.

Elixir-UK town meeting

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ELIXIR-UK would like to invite anyone interested in finding out more about ELIXIR to come to a Town Meeting being held at the Earlham Institute on the afternoon of 1 February. The meeting is designed to provide more information about ELIXIR’s activities both in the UK and internationally and will give an opportunity to discuss and ask questions. The meeting will be followed by a mixer session to allow you to meet the people involved. Attendance is free but registration is required so that we have a good idea of numbers. Please see http://earlham.ac.uk/elixir-uk-town-meeting for more details.

ELIXIR-UK expands to data, tools and interoperability

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ELIXIR-UK, the UK Node in ELIXIR, has completed a reorganisation to better represent the activities of the UK bioinformatics community within ELIXIR and to bring the benefit of participation to a wider range of UK institutions. ELIXIR-UK has extended its remit from its original training brief to now provide data, tools and interoperability services within ELIXIR. It has added three specialist training centres at Birmingham and Cambridge University and the Roslin Institute in Edinburgh to its training portfolio and incorporated interoperability services from the Universities of Oxford (BioSharing and ISA Commons) and Cambridge (InterMine).

Its new Data and Tools resources fall under four categories: Protein Structure and Function (Imperial College, UCL and Dundee University), Expression Atlases (Edinburgh, Heriot Watt and Newcastle Universities), Human Health and Disease (Edinburgh University), and Farmed Animal and Plants (Rothamsted Research and The Roslin Institute). These areas reflect strengths and priorities within the UK. Fuller details on the new Node portfolio can be found on the recently updated ELIXIR-UK web site.

The new composition of ELIXIR-UK was determined by an open and transparent process set up by the Node and was undertaken throughout 2015-2016. The review process brought in external experts to evaluate Expressions of Interest to join the Node, which were either added to the Node immediately or placed on a roadmap for future inclusion. ELIXIR-UK expects to continue this process to include more resources in future. ELIXIR’s SAB reviewed the updated Node application during its summer meeting and welcomed the expansion of the Node and the inclusion of new services. The ELIXIR Board approved the revised ELIXIR-UK remit during its November 2016 meeting.

More about Elixir UK:

https://www.elixir-europe.org/about/elixir-uk

 

Dr Gabriella Rustici is the new Deputy Head of Node

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ELIXIR-UK is pleased to announce the appointment of Gabriella Rustici as its new Deputy Head of Node. Dr Rustici is Bioinformatics Training Manager for the School of Biological Sciences of the University of Cambridge and leads on developing standards and best-practice guidelines for the assessment of training quality and impact within ELIXIR-UK. She will take the lead on building the ELIXIR-UK community as well as working closely with Carole Goble (Head of Node) and John Hancock (Node Coordinator) in the day-to-day running of the Node. For more detail about Gabriella see http://www.elixir-uk.info/team/gabriella-rustici.

CORBEL: Open Call for Research Projects

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Dear colleagues, I’m contacting you on behalf of the EU project CORBEL to which your research infrastructure / your institute is a partner.

The Open Call for Research Projects, organised by WP4, will be launched on October 5, 2016; selected researchers will then have the unique opportunity to gain open access to state-of-the-art technologies and services offered by these research infrastructures across biological and medical sciences.

In order to distribute this news to a broad audience, we would like to ask for your support:

I would like to ask whether it is possible to place the attached announcement on your website. In addition to the plain text, we also prepared an animated GIF/an Apply-Now button to attract the reader.Would it be possible to also add one or both figures to your website?

It would be nice if the announcement could be presented on your website until end of November (call deadline: November 30).

In case you distribute a regular newsletter, we would highly appreciate if you could include the attached contribution.

In addition, we provide a flyer and some PPT slides addressing the Open Call. It would be nice if you could distribute the flyer to interested colleagues and use the PPT slides during upcoming presentations.

Many thanks for your support!

 

Manuela Schuengel (WP2)

Frauke Leitner (WP4 project manager)

Marie Vidal (WP4 project manager)

 

ELIXIR-UK and the UK EU Referendum

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On Thursday 23rd June the UK voted to leave the European Union. In light of this ELIXIR issued the following statement in consultation with ELIXIR-UK:

“In light of the decision by the UK to leave the European Union (EU), ELIXIR would like to clarify that it is not part of the EU: the result does not affect UK membership of ELIXIR, nor have any direct bearing on ELIXIR's ability to access EU research funding. The ELIXIR Hub uses the legal model of EMBL, which is itself an international treaty organisation. It is entirely separate from the EU and a statement from EMBL clarifies this in detail.

The UK has not voted to leave EMBL or ELIXIR. The operational budget of the ELIXIR Hub can continue to be committed on Commissioned Services carried out between the UK and other ELIXIR Members.

Furthermore, for the purposes of participating in EU research programmes, the ELIXIR Hub is categorised as an international treaty organisation (EMBL) rather than a UK entity. The ELIXIR Hub and EBI can still continue to access grants from Horizon 2020 and there will be no impact on the ELIXIR-EXCELERATE and CORBEL grants that are coordinated by the ELIXIR Hub on behalf of partners.

Whilst the ELIXIR UK Node is made up of UK legal entities, there are not expected to be any short term impacts on its activities and operations.”

ELIXIR-UK continues to operate as a node of ELIXIR, participating fully in ELIXIR’s activities, and is moving ahead with its plan to expand its services remit within ELIXIR. We do not expect any change in our remit to represent the UK within ELIXIR.

 

Carole Goble

Head of Node

ELIXIR-UK

Vacancy for ELIXIR technical lead for Data and Interoperability

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The ELIXIR Hub are looking for an experienced and dynamic bioinformatician with strong interest and solid knowledge of semantic technologies in the life sciences to join ELIXIR as the technical lead for data management and interoperability.

Your main task would be to provide day-to-day project management and technical leadership for the ELIXIR Interoperability platform. You would work with partners in ELIXIR member states and our core data resources to ensure interoperable and long-term viable data and metadata management approaches within the ELIXIR infrastructure. This involves mapping current and emerging data management practices, interoperability services and standards. Working closely with and supporting our international scientific leadership team for data interoperability you would play a key role in the development of a long-term interoperability strategy and architecture for ELIXIR.

 

Click here to see more details about this vacancy

Call for Submissions: 4th Workshop on Sustainable Software for Science: Practice and Experiences

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4th Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)
 
 
Location: School of Computer Science, Kilburn and IT Buildings, University of Manchester, Manchester, UK

 

Dates: 2 ½ days from Sept. 12th noon – Sept. 14th 5 pm, 2016 Immediately preceding and co-located in Manchester with First Conference of Research Software Engineers (RSE Conference) (Sept 15-16 at Museum of Science and Industry, Manchester, UK)
 
 
Follow @wssspe, tweet with #wssspe
 
 
A nominal registration fee may be charged.
 
 
Abstract:
 
Progress in scientific research is dependent on the quality and accessibility of research software at all levels. It is now critical to address many new challenges related to the development, deployment, maintenance, and sustainability of open-use research software: the software upon which specific research results rely.  Open-use software means that the software is widely accessible (whether open source, shareware, or commercial).
 
Research software means that the choice of software is essential to specific research results; using different software could produce different results.
 
 
In addition, it is essential that scientists, researchers, and students are able to learn and adopt a new set of software-related skills and methodologies. Established researchers are already acquiring some of these skills, and in particular, a specialized class of software developers is emerging in academic environments who are an integral and embedded part of successful research teams. WSSSPE provides a forum for discussion of these challenges, including both positions and experiences, and a forum for the community to assemble and act.
 
 
WSSSPE4 will consist of two separate tracks with some joint sessions:
 
Track 1 – Building a sustainable future for open-use research software has the goals of defining a vision of the future of open-use research software, and in the workshop, initiating the activities that are needed to get there.
The idea of this track is to first think about where we want to be 5 to 10 years from now, without being too concerned with where we are today, and then to determine how we can move to this future.

 

Track 2 – Practices & experiences in sustainable scientific software has the goal of improving the quality of today’s research software and the experiences of its developers by sharing practices and experiences.  This track is focused on the current state of scientific software and what we can do to improve it in the short term, starting with where we are today.
 
 
Topics of interest include but are not limited to:
 
Development and Community
• Best practices for developing sustainable software
• Models for funding specialist expertise in software collaborations
• Software tools that aid sustainability
• Academia/industry interaction
• Refactoring/improving legacy scientific software
• Engineering design for sustainable software
• Metrics for the success of scientific software
• Adaptation of mainstream software practices for scientific software • Professionalization
• Career paths
• RSE as a brand
• RSE outside of the UK or Europe
• Increase incentives in publishing, funding and promotion for better software • Training
• Training for developing sustainable software
• Curriculum for software sustainability • Credit
• Making the existing credit and citation ecosystem work better for software
• Future credit and citation ecosystem
• Software contributions as a part of tenure review
• Case studies of receiving credit for software contributions
• Awards and recognition that encourage sustainable software • Software publishing
• Journals and alternative venues for publishing software
• Review processes for published software • Software discoverability/reuse
• Proposals and case studies
 
Reproducibility and testing
• Reproducibility in conferences and journals
• Best practices for code testing and code review
 

 

Important Dates:
• Submission of lightning talks: July 10
• Submission of Track 1 idea papers: July 10
• Submission of Track 2 position papers, experience papers, presentations of previously published works, and demos: July 10
• Submission of travel support requests: July 10
• Lightning talk decisions announced: Aug 1
• Track 1 idea papers decisions announced: Aug 1
• Track 2 position papers, experience papers, presentations of previously published works, and demo decisions announced: Aug 1
• Travel support decisions announced: Aug 2
 
 
Submission types and formats:
• Lightning talks: a short paper, up to 2 pages, that if accepted can be conveyed in a 5 to 7 minute talk,
either on Track 1: Building a sustainable future for open-use research software or Track 2: Practices & experiences
in sustainable scientific software.  Lightning talks may be based on either novel or previously published work, but
must contain a core idea that will contribute to the discussion in the workshop.
• Idea papers: a longer paper, up to 8 pages, that presents implementable proposals related to Track 1: Building a
sustainable future for open-use research software. Track 1 participants will build on the proposals and ideas in
these papers, with the goal of initiating the planning, development, and execution of some of the ideas during the
workshop itself. Given the magnitude and importance of the task at hand, the WSSSPE4 organizing committee
encourages these proposals to be developed on an open, public, and inclusive basis. Submitters are invited to
present a vision of some aspect of the future of open-use research software, and a plan of activities to gather and
organize the resources needed to get there.
 
 
Example idea paper topics:
• Adaptation of industrial software engineering principles into the research software community with a plan to
fund the work
• Funding and scaling software carpentry style training in advanced topics
• Infrastructure and funding for community maintenance of open use research software
• Scaling the SSI beyond the UK
• Specific proposals of how to bridging/network the various research software engineering communities in scalable
manner without destroying independence and unique foci of each community
 
• Position papers: a longer paper, not previously published, up to 8 pages, that if accepted can be conveyed in
a 15 to 20 minute talk, on Track 2: Practices & experiences in sustainable scientific software, specifically discussing
what we can do to improve sustainable scientific software in the short term, starting with where we are today.
 
• Experience papers: a longer paper, not previously published, up to 8 pages, that if accepted can be conveyed
in a 15 to 20 minute talk, on Track 2: Practices & experiences in sustainable scientific software, specifically discussing
current practices and experiences and how they have been used to improve the quality of today’s research software
and/or the experiences of its developers.
• Presentation of previously published work: a short paper, up to 2 pages, that if accepted can be conveyed in
a 15 to 20 minute talk, describing a previous published work by the authors and its relevance to Track 2: Practices &
experiences in sustainable scientific software on the topic of improving the quality of today’s research software and
the experiences of its developers by sharing practices and experiences.
• Demos: a short paper, up to 2 pages plus 2 pages of screenshots, that if accepted can be conveyed in a 10 to
15 minute demonstration, showing a tool or process relevant to Track 2: Practices & experiences in sustainable
scientific software, that improves the quality of today’s research software and/or the experiences of its developers.
Demo submissions may be based on previously published work.
 
Submission process:
All submissions should be created in PDF format.  They should begin with a title, author names and affiliations, a short abstract, then the body of the submission.  The title should begin with “Lightning talk:” or “Position paper:” or “Experience paper:” or “Idea paper:” or “Previously published:” or “Demo:”.  Submissions should also include a statement of their license, preferably CC BY 4.0.  Submissions should be made viahttps://easychair.org/conferences/?conf=wssspe4.
 
WSSSPE4 accepted submissions (except presentations of previously published work) will be published by WSSSPE as a special collection inhttp://ceur-ws.org/.  Authors retain copyright to their work and are free to self-publish their submissions or accepted papers elsewhere in addition.
 
 
Preliminary Agenda:
  
Sept 12 pm – Joint session of both tracks
 
Introduction
Keynote
Lightning talks
Updates on actions and activities from WSSSPE3 working groups
Discussion and planning for the remainder of WSSSPE4

 

Sept 13 (all day) and 14 (until 3 pm) – Parallel tracks
 
Track 1: This will be a set of working sessions with a facilitated discussion, breakout sessions, report backs, and active
writing towards the track goal of defining a vision of the future of open-use research software, and a plan of activities that
are needed to get there.
Track 2: presentations of position papers, experience papers, previously published works, and demos; and breakout
sessions or unconference sessions.
 
 
Sept 14 (1:30 pm – 5 pm) – Joint session of both tracks
 
Panel on best practices
Summary and discussion of each tracks’ progress
Planning for future events
 

 

Organizing Committee:
• Gabrielle Allen, University of Illinois Urbana-Champaign, USA
• Jeffrey Carver, University of Alabama, USA
• Sou-Cheng T. Choi, Illinois Institute of Technology, USA
• Tom Crick, Cardiff Metropolitan University, UK
• Michael R. Crusoe, Common Workflow Language project
• Sandra Gesing, University of Notre Dame, USA
• Robert Haines, University of Manchester, UK
• Michael Heroux, Sandia National Laboratory, USA
• Lorraine J. Hwang, University of California, Davis, USA
• Daniel S. Katz, University of Illinois Urbana-Champaign, USA
• Kyle E. Niemeyer, Oregon State University, USA
• Manish Parashar, Rutgers University, USA
• Colin C. Venters, University of Huddersfield, UK
 
 
Program Committee:
(in progress, see web site for additions)
• David Abramson, University of Queensland, Australia
• Lorena A. Barba, George Washington University, USA
• Ross Bartlett, Sandia National Laboratories, USA
• Christoph Becker, University of Toronto, Canada
• David Bernholdt, Oak Ridge National Laboratory, USA
• Stefanie Betz, Karlsruhe Institute of Technology, Germany
• Coral Calero, Universidad Castilla La Mancha, Spain
• Ishwar Chandramouli, National Cancer Institute, National Institutes of Health, USA
• Ruzanna Chitchyan, University of Leicester, UK
• Neil Chue Hong, Software Sustainability Institute, University of Edinburgh, UK
• Karen Cranston, Duke University, USA
• Ewa Deelman, Information Sciences Institute, University of Southern California, USA
• Dave De Roure, Oxford e-Research Centre, University of Oxford, UK
• Charlie E. Dibsdale, O-Sys, Rolls Royce PLC, UK
• Alberto Di Meglio, CERN, Switzerland
• Anshu Dubey, Argonne National Laboratory, USA
• Nadia Eghbal, Independent Researcher (via Ford Foundation), USA
• Martin Fenner, DataCite, Germany
• David Gavaghan, University of Oxford, UK
• Mike Glass, Sandia National Laboratories, USA
• Carole Goble, University of Manchester, UK
• Joshua Greenberg, Alfred P. Sloan Foundation, USA
• Michael K Griffiths, University of Sheffield, UK
• James Hetherington, University College London, UK
• Fred J. Hickernell, Illinois Institute of Technology, USA
• Caroline Jay, University of Manchester, UK
• Matthew B. Jones, University of California Santa Barbara, USA
• Nick Jones, New Zealand eScience Infrastructure (NeSI), NZ
• Jong-Suk Ruth Lee, National Institute of Supercomputing and Networking, KISTI (Korea Institute
of Science and Technology Information), Korea
• Sedef Akinli Kocak, Ryerson University, Canada
• James Lin, Shanghai Jiao Tong University, China
• Frank Löffler, Louisiana State University, USA
• Gregory Madey, University of Notre Dame, USA
• Ketan Maheshwari, University of Pittsburgh, USA
• Steven Manos, University of Melbourne, Australia
• Chris A. Mattmann, NASA JPL & University of Southern California, USA
• Abigail Cabunoc Mayes, Mozilla Science Lab, USA
• Robert H. McDonald, Indiana University, USA
• Lois Curfman McInnes, Argonne National Laboratory, USA
• Chris Mentzel, Gordon and Betty Moore Foundation, USA
• Peter Murray-Rust, University of Cambridge, UK
• Christopher R. Myers, Cornell University, USA
• Jarek Nabrzyski, University of Notre Dame, USA
• Cameron Neylon, Curtin University, Australia
• Aleksandra Pawlik, New Zealand eScience Infrastructure (NeSI), NZ
• Fernando Perez, Lawrence Berkeley National Laboratory & University of California, Berkeley, USA
• Marian Petre, The Open University, UK
• Marlon Pierce, Indiana University, USA
• Andreas Prlic, University of California, San Diego, USA
• Karthik Ram, University of California, Berkeley, USA
• Morris Riedel, Juelich Supercomputing Centre, Germany
• Norbert Seyff, University of Zurich, Switzerland
• Arfon Smith, GitHub Inc, USA
• Borja Sotomayor, University of Chicago, USA
• Edgar Spalding, University of Wisconsin, USA
• Maria Spichkova, RMIT University, Australia
• Victoria Stodden, University of Illinois Urbana-Champaign, USA
• Matthew Turk, University of Illinois Urbana-Champaign, USA
• Ewout van den Berg, IBM Watson, USA
• Nancy Wilkins-Diehr, San Diego Supercomputer Center, University of California, San Diego, USA
• James Willenbring, Sandia National Laboratories, USA
• Scott Wilson, Cetis LLP, UK
• Theresa Windus, Iowa State University and Ames Laboratory, USA

New MOOC from Manchester - Clinical Bioinformatics: Unlocking Genomics in Healthcare

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This free online course aims to raise awareness amongst healthcare professionals of the role of Clinical Bioinformatics and Genomics in healthcare today. We will illustrate how the discipline of Clinical Bioinformatics provides an important bridge between the cutting edge science and the delivery of genomic medicine in clinical practice. By understanding the role of a Clinical Bioinformatician it will become clear how integral they are to ensuring the beneficial opportunities of genomic medicine are fully realised in patient care

 

Please click here to find out more. This course starts on the 6th of June.

Vacancy: Bioinformatics Training Impact Co-ordinator (Fixed Term) - Cambridge

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The Bioinformatics Training Facility of the School of Biological Sciences, University of Cambridge (UoC) is looking for a Training Impact Co-ordinator. The post-holder will develop (building on existing work), implement, monitor, analyse and report on a comprehensive system of training metrics/key performance indicators across the portfolio of ELIXIR (http://www.elixir-europe.org/) and EXCELERATE (https://www.elixir-europe.org/news/elixir-accelerates-major-horizon-2020-funding) bioinformatics training activities.

FInd out more - Click here to visit the job page at Cambridge Univeristy

WILL YOUR RESOURCE OR TOOL BE PART OF ELIXIR-UK’S FUTURE?

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ELIXIR-UK invites present and future participants in ELIXIR who wish to provide data resources or tools to ELIXIR as part of the UK ELIXIR Node to attend a webinar at 2pm on Tuesday 9th February to learn more about ELIXIR, ELIXIR-UK and the process being put in place to expand ELIXIR-UK’s portfolio. You can join the webinar using this link. The webinar will be followed up by a workshop at the Wellcome Trust on 1st March to provide more detailed information about the process and how to develop an Expression of Interest.

For more detail see this web page

For more information contact John Hancock (ELIXIR-UK Node Coordinator) john.hancock@tgac.ac.uk

ELIXIR Workshop

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19th – 21th January 2016. Hosted by ELIXIR-EBI at Hinxton, these workshops brought together training representatives from 6 ELIXIR nodes (including Rita Hendricusdottir, Gabry Rustici and Lee Larcombe from ELIXIR UK) and from external organisations including BD2K, Data carpentry, Cold Spring Harbour and Intel. There was much lively discussion across the three days, resulting in quite a lengthy list of actions!

The first half of the workshop focused on the development of a Train the trainer programme specifically designed for ELIXIR trainers, taking inspiration from EMBL-EBI and Software/data carpentry initiatives; whilst the discussions during the second half reviewed current methods being employed for assessment of training quality and impact and the role of training in increasing ELIXIR impact more generally.

One major outcome of this workshop is the date of the Train the trainer pilot (a series of 6 workshops) launch in May 2016, further details for this first pilot will be sent out in due course.

Image: Dr Gabry Rustici - Cambridge University, UK with Dr Sarah Morgan - EMBL-EBI leading the Excelerate Training Quality and Impact workshop

UK Head of Node Steps Down

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Professor Chris Ponting is stepping down as of today from his role as Head of the ELIXIR UK Node.  Chris remains fully committed to ELIXIR-UK and to the ELIXIR project, and continues to jointly lead on training activities within the UK Node and the ELIXIR Training platform. Chris has been Head of the UK Node since its initiation in 2012, successfully overseeing its establishment as leaders in training across ELIXIR and the development of its important role in ELIXIR’s Interoperability platform while initiating planning for the Node’s future development.

Interim arrangements have been put in place whereby the Deputy Head of Node, Professor Carole Goble, will take on the role of Head of Node working closely with John Hancock, ELIXIR-UK’s Node Coordinator.

 

Contacts: Carole Goble (carole.goble@manchester.ac.uk), John Hancock (john.hancock@tgac.ac.uk).

COURSE ANNOUNCEMENT: Protein Networks and Systems Biology - ELIXIR-ITA

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ELIXIR-ITA, in collaboration with the University of Bologna (IT) is pleased to inform you that the applications for the upcoming training course onProtein Networks and Systems Biology are open.

Full details at: http://bioinformaticstraining.pythonanywhere.com

Keynote Speakers:
Prof. Rita Casadio (Università di Bologna, IT)
Prof. Gianni Cesareni (Università di Roma "Tor Vergata", IT)

Instructors:
Luana Licata (Università di Roma "Tor Vergata", IT)
Alberto Calderone (Università di Roma "Tor Vergata", IT)
Pier Luigi Martelli (Università di Bologna, IT)
Piero Fariselli (Università di Bologna, IT)
Allegra Via (Sapienza Università di Roma, IT)
Andreas Zanzoni (INSERM, Marseille, FR)

IMPORTANT DATES for this Course:
Deadline for applications: 30th November 2015
Start of candidate selection process: 15th November 2015
Course date: 14-18 December 2015
Venue: Dept. of Computer Science and Engineering IT Room (University of Bologna) - Via Ranzani 14/C, Bologna, IT
Fee: Free

Candidate selection will start on November the 15th and those with an adequate profile will be accepted immediately, especially if they come from other countries (to allow them to find reasonably cheap flight tickets). Priority will be given to candidates from ELIXIR-ITA member institutions (see the list at the bottom) and ELIXIR nodes.

Course description
The aim of this course is to familiarise the participants with the different approaches to the study of protein-protein interactions (PPIs), protein interaction networks and systems biology, providing hands-on training sessions as well. The course is structured in four sessions. The first one focuses on bioinformatics databases, tools, and web resources dedicated to PPIs. The second one provides a molecular point of view on protein-protein interactions (PPI), including how to exploit structural information in analyses and predictions. The third session is about graph theory, biological system modelling and tools to analyse PPI networks. Last session is about biomedical applications of PPI resources, methods and networks.

This course is aimed at students in master degree courses, PhD students, post-doctoral researchers and PIs who are working or planning to work in the field of protein interactions, protein interaction networks and/or systems biology. It consists of invited lectures, theory and practicals. Lectures, provided by invited speakers and instructors, are open to everyone provided they reserve one sit in advance. Practicals are limited to 20 participants.

Thank you for your interest,

The course organisers

Alberto Calderone (University of Rome Tor Vergata, IT)
Giuseppe Profiti (University of Bologna, IT)
Allegra Via (Sapienza University of Rome, IT)

ELIXIR-UK Questionnaire on UK Community Engagement

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ELIXIR-UK is carrying out a survey to help it in developing its future strategy. The questionnaire addresses the level of awareness of ELIXIR’s and ELIXIR-UK’s activities in the UK and how it can best engage the wider UK community with an interest in ELIXIR’s development, activities and facilities. ELIXIR-UK would therefore like to invite all researchers who make use of international data resources in the life sciences to complete this short questionnaire (10 questions).

 

The questionnaire can be found at https://www.surveymonkey.com/r/Z28BSVG.

BioSB Course on Managing and Integrating Life Science Information: Approaches using Linked Data and Semantics (4th edition)

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Course coordinators: Marco Roos, Katy Wolstencroft

Date
: 30 November – 4 December 2015 
Location: SURF, Utrecht, the Netherlands
Website: http://biosb.nl/education/course-portfolio/course-managing-and-integrating-information-in-the-life-sciences/
Registration: http://biosb.nl/education/course-portfolio/course-managing-and-integrating-information-in-the-life-sciences/enrollment-milsi-2015/ .Please not that this course is free of charge for PhDs who are or will become a member of the  BioSB research school, and with a reduced fee for other researchers who are or will  become a member of BioSB. More information about the BioSB membership can be found here:http://biosb.nl/about/members/biosb-membership-information/ .
Course flyerhttp://biosb.nl/wp-content/uploads/2013/08/Wolstencroft_Roos_Course_2015_June.pdf


Target audience

This course is for bioinformaticians who would like to learn about leading-edge data and knowledge integration solutions. You will learn (1) powerful and flexible approaches to data and information management for your bioinformatics application (Semantic Web and Linked Data), (2) how to work with data across remote locations, for instance by applying Web Services and workflows, (3) how to publish your own data to make it available and reusable for the rest of the community. We assume a basic understanding of bioinformatics programming for the hands on sessions. It would suit previous user participants of BYOD meetings who would like more hands-on experience of data integration. It would also suit data providers who would like to explore new ways of serving their data or integrating it with other resources

Description
The amount of Life Science data available in the public domain is a vast and growing resource for bioinformatics research. There are over 20 million papers in PubMed and over 1600 biological databases. In many cases finding and applying the information from these resources is far from trivial. Following this course will show you techniques for working with these distributed resources, which includes using the web of Linked data and scientific workflows. It will also focus on methods for using or linking your own data into this large distributed Semantic Web of resources, in order to ensure that your data is FAIR (Findable, Accessible, Interoperable and Reusable).

This course introduces modern techniques for the management of life science data and knowledge for bioinformatics applications. After following this course students should be able to start creating their first applications based on these technologies or make more informed design decisions for their current application.

In this course you will learn about:

1.       Linked Data and the Semantic Web technologies that underpin it

2.       How you can use Linked Data for data and knowledge integration in the Life Sciences

3.       Available Linked Data resources in the public domain and large-scale projects that use these resources

4.       How you can integrate your own data with Linked Data resources

5.       How you can combine data integration and analysis over distributed resources, using Web Services and workflows


Lecturers:
 Marco Roos, Katy Wolstencroft, Frank van Harmelen, Paul Groth, Simon Jupp, Jesse van Dam, and others TBC
.
Programme

Monday 30/11 – Introduction to Semantic Interoperability and the Semantic Web

09:00-09:30 Coffee/Tea
09:30-09:45 Introduction and workshop goals
09:45-11:00 Semantic Web Primer
11:00-11:15 Coffee/Tea
11:15-12:30 An introduction to Linked Data
12:30-13:00 Lunch
13:00-15:00 Introduction to creating RDF and using a triple store (hands on session)
15:00-15:30 Surf Sara services for researchers
15:30-…….. Welcome drinks

Tuesday 01/12 – The Semantic Web in Use

09:30-10:00 Define course projects/interests (BYOD)
10:00-10:45 An Introduction to Constructing SPARQL Queries
10:45-11:00 Coffee/Tea
11:00-12:30 SPARQL hands-on session
12:30-13:30 Lunch
13:30-14:30 An Introduction the the EBI RDF platform and Ontologies
14:30-16:30 Querying the EBI RDF platform, hands-on

Wednesday 02/12 – The Semantic web in use – systems and guidelines

09:30-10:30 The OpenPHACTS project
10:30-10:45 Coffee/Tea
10:45-12:30 Openphacts hands on session
12:30-13:30 Lunch
13:30-14:30 Guidelines and best practices for Linked Data
14:30-16:30 Hands on session
16:30-17:00 Wrap-up

Thursday 03/12 – Making Data Understandable and Searchable

09:30-10:30 An Introduction to Describing and Annotating Data: Case Study in systems Biology
10:30-10:45 Coffee/Tea
10:40-12:30 Using tools for annotating and describing data – hands on session
12:30-13:30 Lunch
13:30-14:30 Ontologies in depth
14:30-16:30 Ontology hands-on
16:30-17:00 Wrap-up

Friday 04/12 – Using, Integrating and Analysing Data

09:30-10:30 An introduction to scientific workflows and distributed analyses
11:00-12:30 Designing and executing Taverna Workflows, hands-on
12:30-13:30 Lunch
13:30-15:00 Hands-on: Data integration with linked data (BYOD wrap up)
15:00-15:30 BYOD reports
15:30-16:15 The added value of FAIR data – Closing keynote
16:15-16:45 Wrap-up

ELIXIR UK-chaired StaTS project reports to stakeholders

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London, October 1st: Dr Lee Larcombe reported progress on the Statistics Training Signposting project (StaTS) at the Science Industry Partnership (SIP) Stakeholder meeting, coinciding with the SIP project's 1st year report

Progress was also reported later that day, to the Association of British Pharmaceutical Industry (ABPI) academic liaison expert network group.

The StaTS project Working Group and Expert Panel, chaired by Dr Larcombe of ELIXIR UK represent efforts to coordinate national efforts to address the shortage of statistical skills amongst the UK science base.

Click here to read more details on the development and progress of the StaTS project

"Evidence-Based Teaching: What We Know and How to Use It" by Greg Wilson at University of Cambridge

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University of Cambridge will be running an workshop on "Evidence-Based Teaching: What We Know and How to Use It" where Greg Wilson (from Software and Data Carpentry) will be addressing questions such as:

  • What are the cognitive differences between novices, competent practitioners, and experts?
  • Do different people really have different learning styles?
  • Do flipped classrooms actually work better than regular lectures?

The workshop will explore recent research in these areas and more, and show participants how to apply the outcomes of this research in the classroom to improve teaching.

When: Wednesday 30 September 2015, 1.00 - 4.00 pm

Where: Biffen lecture theater, Department of Genetics, on the Downing site.

Greg Wilson has been studying an applying evidence-based teaching for many years. He is the co-founder and Executive Director of Software Carpentry [4], a crash course in computing skills for scientists and engineers. He has worked for 30 years in in both industry and academia, and is the author or editor of several books on computing (including the 2008 Jolt Award winner "Beautiful Code") and two for children. Greg received a Ph.D. in Computer Science from the University of Edinburgh in 1993.

To register, visit http://training.csx.cam.ac.uk/bioinformatics/event/1561050

For more information, please contact Gabriella Rustici (gr231@cam.ac.uk) or Laurent Gatto (lg390@cam.ac.uk).

Dr Tim Stitt joins ELIXIR UK as Compute Coordinator

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The ELIXIR UK Exec Committee are pleased to appointed Dr Tim Stitt, Head of Scientific Computing at TGAC, as the Compute Coordinator for the UK node

From Tim's biog at TGAC: "A native of Belfast, Northern Ireland, Tim has over 15 years experience in High-Performance Computing and Parallel Programming. After earning a PhD in Computational Physics from Queen's University Belfast, Tim has applied his HPC knowledge at various HPC centres worldwide including ICHEC (Ireland), CSCS (Switzerland) and CRC (USA). Along the way, Tim has held faculty positions in Computer Science and Civil Engineering whilst teaching parallel computing to undergraduate students at the University of Notre Dame (USA). Tim has also held committee roles within the European PRACE and US XSEDE supercomputing projects."

ELIXIR Software and Data Carpentry Pilot: Instructor Training

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The workshop is a part of ELIXIR Software and Data Carpentry Pilot Project. The trainers will be Tracy Teal (Data Carpentry Executive Director) and Aleksandra Pawlik (University of Manchester, Software Sustainability Institute).  The workshop will focus on developing teaching skills and approaches to effective training. We will cover the basics of educational psychology and instructional design, and look at how to use these ideas in both intensive workshops and regular classes. The attendees will also learn how to work with Data and Software Carpentry infrastructure for setting up and running workshops, contributing to training materials and interacting with the instructor community. The training will involve some pre- and post-workshop homework (some reading and tasks to complete).

Please note that the attendees are responsible for their travel expenses. 

It is strongly encouraged that the attendees have had some previous exposure to the Data and Software Carpentry workshops, either as students, helpers, observers or co-instructors. If you would like to become an Instructor but have not yet participated in any workshop, we encourage you to check the list of upcoming Software and Data Carpentry workshops to see if you could join any of these events. 

If you would like to attend the training, please contact Aleksandra Pawlik.

Research Software Engineers - University of Oxford

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The life science group at University of Oxford’s e-Research Centre is looking for motivated individuals with software engineering experience (web application frameworks and/or backend development) and leadership ability to contribute to:

  1. a growing portfolio of data and knowledge management projects funded by several UK, EU, NIH and pharma-funded projects,
  2. infrastructure activities for the ELIXIR-UK node of the ELIXIR-EXCELERATE programme, and
  3. two NIH Big Data to Knowledge Initiative’s centres around data indexing and metadata registry.

More details are available here.

ELIXIR-UK Genome Assembly and Annotation Questionnaire

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On behalf of the ELIXIR-UK, we would like to invite colleagues in the UK to complete a short questionnaire on the topic of Genome Assembly and Annotation.

A vital part of the UK's involvement in ELIXIR, the European Infrastructure for Life Science data, is building a knowledgebase about the UK's expertise in bioinformatics infrastructure (including hardware, software and people).  Such a knowledgebase will allow the UK node to better represent the UK's interests.

A series of workshops is being run within ELIXIR as part of the "Capacity Building in Genome Assembly and Annotation" work package of theEXCELERATE project. One is on the topic of "Genome Assembly and Annotation". We are therefore asking anyone involved in genome assembly and annotation within the UK to fill in a short survey which can be found at the following URL: https://www.surveymonkey.com/r/R8KYH8Z. As we wish to get the best possible coverage, we would be grateful if you would pass on this request to any colleague who you think could contribute.

Mick Watson and Chris Ponting on behalf of ELIXIR-UK

ELIXIR-UK and Software and Data Carpentry are organising two instructor training workshops

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ELIXIR-UK and Software and Data Carpentry are organising two instructor training workshops that offer trainees an insight into how to train a life science audience in computing:

  1. 8-9 October, UCL, London: http://anenadic.github.io/2015-10-08-instructor-training-ucl-london/
  2. 23-24 November, Manchester: http://anenadic.github.io/2015-11-23-instructor-training-manchester/


The workshops are led by Greg Wilson, the founder of Software Carpentry and a Steering Committee member of its sibling Data Carpentry currently on sabbatical in the UK. The workshops aim train volunteer instructors to deliver computing training to their fellow life scientists by presenting best-practice on how to deliver training in programming. The workshops are suited for people who have already gone through a Software or Data Carpentry workshop, either as a trainee or as a helper.

Greg will introduce basic concepts from educational psychology and instructional design, and look at how to apply these ideas in both intensive workshops and regular classes. The workshops also actively encourage the potential instructors to develop networks that they can later use to share experiences, good and bad, and so collaboratively refine the training that they offer.

ELIXIR UK Data Carpentry Workshop, Cambridge

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Designed to teach basic concepts, skills and tools for working more effectively with data, the workshop aims at life-science researchers with little or no prior knowledge of programming, scripting, or command line tools.

It is hosted by the University of Cambridge, UK.

Workshop learning objectives and programme

  • How to use spreadsheet programs (such as Excel) more effectively, and the limitations of such programs
  • Getting data out of spreadsheets and into more powerful tools (R)
  • Data management and manipulation
  • Data visualization
  • Workflows and automating repetitive tasks, in particular using the command line shell

ISMB 2015, Dublin - The Tech Highlights

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The ISMB conference ran from Sunday 12th to Tuesday 14th July 2015 in the Dublin Conference Centre, Ireland. Well over 1000 molecular biologists from a variety of sub-domains, experience-levels, and backgrounds banded together to exchange knowledge, present their research, promote their infrastructure and software, and converse with like-minded scientists.

Many of the speakers, poster sessions, and break-out groups discussed themes such as training, infrastructure, and technology; with a strong presence from ELIXIR in each. You can barely turn your head in the forum area without setting your eyes upon an ELIXIR representative sporting the ‘DATA FOR LIFE’ T-Shirt; deep in conversation with attendants about our activities.

Here's a summary of some of my favourite presentations on tech at this years ISMB.  

 

What’s new in the Galaxy (Project) (Dave Clements)

Dave presented a great overview of the latest features from the frontlines of the seemingly ubiquitous Galaxy (https://galaxyproject.org/) project. These features were very warmly welcomed by the audience with several comments and questions echoing just how useful these changes will be to their current work (including high-praise from following presenter Audrey Michel of the RiboGalaxy project). The presentation included such new features as:

  • multi-sample analysisImage result for galaxy workflow

  • user interface improvements

  • tool usage and definition updates

  • using Docker for tool integration

  • integration with interactive environments.

 

FAIRDOM: FAIR data and model management in Systems Biology (Carole Goble)

Image result for fairdom

ELIXIR-UKs own Carole Goble gave an impressive presentation about the feature-rich research management platform FAIRDOM. FAIRDOM (http://fair-dom.org/) enables the systems biology community to produce Findable, Accessible, Interoperable and Reproducible Data, Operating procedures and Models.

Heterogeneous data and models from systems investigations can be aggregated and interlinked in the central FAIRDOMHub, for stewardship and publication, or in a local FAIRDOM instance, for collaboration and sharing.

 

GenomeSpace: An environment for frictionless bioinformatics (Sara Garamszegi)

Image result for genomespace

Sara Garamszegi from The Broad Institute gave a fascinating talk about her project GenomeSpace (http://genomespace.org/). GenomeSpace is a platform that supports an open community of genomics analysis tools. Using GenomeSpace, researchers can construct analyses requiring communication and data transfer between diverse tools such as Web applications and client-side tools. GenomeSpace supports cloud-based storage, handles file format compatibility issues automatically, and enables reproducibility of multi-tool analyses.

GenomeSpace also provides ‘recipes’ which concisely and clearly instructs users how to interoperate their data between GenomeSpace and the different supported tools.

 

BioJS 2.0: more flexible, modular, open web biological visualization (Manuel Corpas)

Image result for biojs

Another ELIXIR member Manuel ‘Manny’ Corpas, the Technical Co-ordinator for ELIXIR-UK, gave a great, succinct presentation on his project: BioJS (http://biojs.net/). He started with an overview of the BioJavaScript library for the visualisation of biological data, and then delved into some of the latest updates including the adoption of the NPM package manager, browserify and several other JavaScript technologies. I must say, the new interface is looking very modern, well done Manny!



 

“ISA as a FAIR research object” Hack-the-Spec event

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The ISA Commons moderators are organising a Hack-The-Spec event from 20th to 22th July 2015 at the University of Oxford, as part of the ELIXIR UK Node activities and with the participation of members of the ISA user community, ELIXIR EBI and NL Nodes, FAIRDOMRO and Nanopublicationsgroups. The event is organised thanks to funding from BBSRC UK-China award BB/J020265/1.

 

ISA stands for Investigation/Study/Assay and refers to the ISA framework, a community-driven metadata tracking framework to facilitate standards-compliant collection, curation, management and reuse of datasets in an increasingly diverse set of life science domains. The ISA framework is also part of the ELIXIR UK node interoperability components of the EXCELERATE project.

 

The objectives of the event is to focus on the ISA specification as a FAIR research object. We will address the need for an updated design and documentation that enabling for evolutions while maintaining backward compatibility with existing users, partly tools, and conversions to other existing formats.

 

The specific objectives are:

  1. Revise the ISA specification and prepare a new version (2.0) considering the ISA model (with extensions) and multiple serialisations, including tabular, RDF (see linkedISA, doi: 10.1186/1471-2105-15-S14-S4) and JSON.

  2. Collect and review use cases for extension - What is missing in the current ISA ? Provide use case and tell us why you need it.

  3. Establish implementation guidelines for creating and distinguish between each of the following:

    1. ISA design patterns

    2. ISA configurations

    3. ISA extensions

    4. RO, ISA and nanopublications (see doi: 10.1371/journal.pone.0127612 )

 

The confirmed attendees to the event are representative set of ISA users, mainly from China and UK or closely related to some ongoing/new funded projects associated with UK teams

  1. Scott Edmunds (GigaScience)

  2. Peter Li (GigaScience)

  3. Rob Davidson (GigaScience)

  4. Chris Hunter (GigaScience)

  5. Nina Jeliazkova (EU Toxbank, EU eNanoMapper)

  6. Reza Salek (ELIXIR-EBI, MetaboLights, EU Phenomenal)

  7. Ken Haug (ELIXIR-EBI, MetaboLights, EU Phenomenal)

  8. Pablo Conesa (ELIXIR, MetaboLights)

  9. Rob Davey (BBSRC COPO, ELIXIR-UK)

  10. Ralf Weber (ELIXIR-UK)

  11. Norman Morrison (FAIRDOM, ELIXIR-UK)

  12. Marco Roos (Nanopublications, ELIXIR-NL)

  13. Susanna Sansone (EU Phenomenal, BBSRC COPO, ELIXIR-UK)

  14. Alejandra Gonzalez-Beltran (EU Phenomenal, BBSRC COPO, ELIXIR-UK)

  15. Philippe Rocca-Serra (EU Phenomenal, BBSRC COPO, ELIXIR-UK)

  16. Alfie Abdul-Rahman (BBSRC COPO)

  17. David Johnson (EU Phenomenal, joining Oxford ISA team from September)

  18. Allyson Lister (BioSharing) - remotely

  19. Egon Willighagen (EU eNanoMapper, ELIXIR-NL) - remotely

  20. Jildau Bouwman (TNO, ELIXIR-NL)  - remotely

ELIXIR Galaxy Working Group Meeting July 7th 2015 @ GCC2015

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ELIXIR Galaxy Working Group Meeting takes place on July 7th 2015 @ Galaxy Conference GCC2015 in Norwich, Genome Seminar Room in TGAC Building, 18:15-20:00.

The Galaxy workflow system is extensively used as part of national infrastructure in several Nodes. Though there are potential synergies and possibilities to collaborate across Nodes, in ELIXIR there is not a common effort to work with Galaxy. In the Galaxy breakout session as well as in the plenary session at the all-hands meeting it was highlighted the usage of Galaxy in ELIXIR is growing and becoming important. As such it was proposed we should have a more coordinated effort to work together with the Galaxy team and represent the ELIXIR position.

ELIXIR Galaxy Working Group proposal document

Software Carpentry get more done in less time

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The aim of this study by Alexandra SimperlerGreg Wilson was to investigate if participants of Software Carpentry (SC) workshops get more done in less time once they go back to their labs. They asked 32 questions to assess 24 former participants to analyse if SC gave them the computing skills to accomplish this. The research shows that time was already saved during the workshop as it could shorten the learning process of new skills. A majority of participants were able to use these new skills straight away and thus could speed up their day to day work.

Read about the study at: http://arxiv.org/abs/1506.02575

ELIXIR examines the use of Galaxy platform in Europe

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ELIXIR is launching an online survey to learn more about how the Galaxy platform is used across the ELIXIR infrastructure and beyond. It is intended for IT experts and developers maintaining and developing Galaxy services. Any Galaxy administrator or developer is invited to take part.

Go to the survey!

Galaxy is a well-established web platform for data analysis in bioinformatics. A great number of ELIXIR nodes use Galaxy as part of their daily operations in their workflows. The survey results will feed into a set of recommendations on the ELIXIR technical strategy with regards to the provision of Galaxy services and infrastructure.

The deadline to complete the survey is 7 July 2015 at 12.00 (noon) BST. The initial results will be discussed and presented at the TGAC face-2-face Galaxy workshop, during the upcoming Galaxy Community conference (6-8 July 2015 in Norwich, UK).

CompBio-Docker Symposium 2015

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Kings College London and the Biomedical Research Centre (BRC) will be running a 2 day Docker in Bioinformatics event on 9-10 November in London.

"Docker is now establishing itself as the de facto solution for containerization across a wide range of domains. The advantages are attractive, from reproducible research to simplifying deployment of complex code. Several bioinformatics groups are now utilizing this for various purposes, we would like to bring together some notable cases to discuss how advantage of this new technology can best be achieved."

Data Carpentry hackathon and workshop at ELIXIR Netherlands

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The hackathon consisted of two days during which the participants representing 10 ELIXIR Nodes worked on Data Carpentry training materials. The first day started with the introduction to Data and Software Carpentry teaching model. This was then followed by a review and discussion on the existing materials. The participants made suggestions about the possible improvements for the existing materials and new topics to be developed. The overall theme of the hackathon was "genomics" and hence the participants could base their work on the existing contents for teaching genomics in Data Carpentry. Eventually three groups were formed:

  • Group 1 which worked on creating training materials on using ELIXIR Cloud resources.
  • Group 2 which worked on a decision tree for using cloud computing.
  • Group 3 which worked on different aspects of understanding how to use one's data for genomics. In particular the group worked on describing the file formats, file manipulation, pipelines integration, post-assembly - de novo RNA Transcriptome Analysis, handling blast annotation output and verifying data.

The hackathon was facilitated by Karthik Ram (University of Berkeley, rOpenSci, Data Carpentry) and Aleksandra Pawlik (University of Manchester, Software Sustainability Institute). After the hackathon Karthik and Aleksandra then taught a 2-day Data Carpentry workshop. It was the first Data Carpentry workshop in Netherlands. 30 students registered to attend it. All of them were from life science research area. The workshop covered the standard Data Carpentry curriculum. One module was added at the end of the second day. This module covered using ELIXIR Cloud resources and was the first time the materials created during the hackathon were used for actual teaching.

The whole event received positive feedback and on the overall this Pilot Project appears to have a great reception within ELIXIR. The Slovenian and Belgian Node are running workshops this year and it is likely that other will follow soon.

ELIXIR-UK's 'IPython Notebook and Jupyter' workshop, 27 May, Manchester

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ELIXIR-UK are piloting the 'IPython Notebook and Jupyter' workshop in Manchester next Wednesday, May 27, 2015.

During the workshop the participants will learn how to use the IPython Notebook for their research purposes - combining executable code to analyse and visualise data with notes, images and other references.

The registration form for the workshop:
http://goo.gl/forms/wEzXSYDYJe

Detailed agenda and related info:
http://apawlik.github.io/2015-05-27-ipynb-workshop/

Introduction to data management planning, DMPonline, and planning for sustainability workshop

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DMPOnline is a Web-based tool (developed by Digital Curation Centre) to help funders and institutions to set up their own DMP templates and researchers write DMPs (by modifying the funders' and institutional templates and creating their own DMPs for their grant applications). Templates can be for different requirements and audiences (even within the same institution) and can have associated tailored guidance that can be discipline-specific (e.g. for bioscience).

DCC ran a workshop on DMP on May 11 in Newcastle, where they gave an introduction to data management planning and DMPonline system, what a data management plan is and how to go about completing one, how to understand funders' requirements for data management and sharing, how to use DMPonline system to customise DMPs by institutions and researchers.

For slides and more details, see:
http://www.dcc.ac.uk/events/workshops/introduction-data-management-planning-dmponline-and-planning-sustainability

    ELIXIR accelerates with major Horizon 2020 funding

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    11 May 2015, Hinxton, UK – ELIXIR has been awarded €19 million from the EU to accelerate the implementation of Europe’s life-science data infrastructure over the next four years. From September 2015, ‘ELIXIR-EXCELERATE’ will facilitate the integration of Europe’s bioinformatics resources, supporting all sectors of life-science R&D. It will deliver excellence to ELIXIR’s users by fast-tracking the development and deployment of essential data services.

    EXCLERATE funding will help ELIXIR coordinate and extend national and international data resources to ensure the delivery of world-leading life-science data services. It will support a pan-European training programme, anchored in national infrastructures, to increase bioinformatics capacity and competency. It will also provide efficiencies in management and operation throughout the infrastructure, which is distributed amongst 17 countries.

    Next event of the "Carpentry Pilot Project" to be hosted by ELIXIR NL

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    The second event of the ELIXIR Pilot Project ”Working up and building the foundation for Data Carpentry and Software Carpentry within ELIXIR” will be hosted by the ELIXIR Netherlands on 22-25th June 2015. The event will be held at the Utrecht University and will be co-run by Karthik Ram (Data Carpentry, University of Berkley and ROpenSci) and Aleksandra Pawlik (Data Carpentry, Software Carpentry and the Software Sustainability Institute at the University of Manchester).

    The event will consist of a two-day hackathon to develop and improve teaching materials for computational methods in life sciences and a two-day Data Carpentry workshop.

    If you are interested in the event, please contact Aleksandra Pawlik.

    TeSS workshop aims to bring together the ELIXIR training community and receive feedback on TeSS training portal.

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    TeSS workshop aims to bring together the ELIXIR training community and present them the TeSS Training Portal, disseminate and promote TeSS activities to stakeholders, receive feedback to better tune the platform to the needs of the community and collect ideas for the future development.

    More details at:
    http://dev.mygrid.org.uk/wiki/display/EL/TeSS+Workshop+@+ELIXIR+All+Hands+Meeting%2C+30+March%2C+Hinxton

    Registration form (registration is free):
    https://docs.google.com/a/mygrid.org.uk/forms/d/1h2DKLNspXj7IskbVf79pI7VKerPzs3xCZ-xoLnUJckw/viewform

    Short courses from the FARR Institute: Harnessing Electronic Health Records for Research

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    An intensive programme of 13 short courses in March 2015

    We are pleased to launch a unique programme of 13 inter-related short courses in the rapidly developing field of electronic health records research, spanning a wide range of basic and applied health research applications.

    Courses are entirely modular to allow individuals to select those most relevant to their research and learning needs.

    What can I learn?

    These courses address the ‘why?’, the ‘what?’ and the ‘how?’ of EHR research and critically evaluate scientific opportunities and challenges, in what is being proposed as a new paradigm in medical research.

    Taught by internationally recognised faculty, they span data-intensive biomedical research across diverse forms of EHR (nationally available data from primary and secondary care), regional data in hospital informatics, as well as genomics as applied to EHR research.

    Who are these courses for?

    The courses are intended for people with from a wide range of backgrounds - including health care, epidemiology, biostatistics, health informatics, NHS IT, bioinformatics, genomics and computer science - and at different career stages, from those thinking of doing an MSc or PhD to established researchers.

    Where is the venue?

    The programme will be delivered in central London at the Farr Institute London, 222 Euston Road, over an intense 3 week period.

     

    Click here for more information at the FARR Inst website

    BBSRC and MRC Review of Vulnerable Skills and Capabilities

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    In August/September 2014 the BBSRC and MRC carried out a consultation on Vulnerable Skills and Capabilities in the biosciences and biomedical sciences.  The report is now available on the BBSRC and MRC websites.

    Over 240 vulnerabilities were reported and both BBSRC and MRC.  After careful review of the vulnerabilities described and consultation with advisory bodies, the cross-cutting themes being prioritised by each council are as follows:

    BBSRC: Maths, statistics and computation skills; Physiology and pathology skills; Agriculture and Food Security skills

    MRC: Quantitative skills; Interdisciplinary skills; Whole organ / organism physiology (full details here)

    Python for Life Scientists course at TGAC, 20-24 April 2015

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    All the course’s examples and practical sessions will focus on solving the following biological problems:

    • Working with DNA and protein sequences Data retrieval from files and their manipulation
    • Running applications, such as BLAST, locally and from a script
    • Finding motifs in sequences Parsing Swiss-Prot files, PDB files, ENSEMBL records, blast output files, etc
    • Biopython will be also be introduced and applied to some of the above examples.

    More details and registration.

    Workshop: Best practice in NGS training - Cambridge Jan 2015

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    An international workshop was held at Cambridge University on the 13th and 14th of January 2015 to bring together an NGS training community to share examples of best practice.

    Delegates came from institutes in the UK and Europe; from USA and Australia; and from ELIXIR-IT, ELIXIR-FI and ELIXIR-EE, as well as those involved from ELIXIR-UK.

    The meeting was a joint Cambridge University, TGAC and ELIXIR-UK event.

    Canadian Bioinformatics Workshop (CBW) series – May/June 2015

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    The CBW is pleased to present its 2015 series of advanced bioinformatics workshops!

     

    • (NEW) Introduction to R: Toronto, May 20, 2015
    • Exploratory Analysis of Biological Data using R: Toronto, May 21-22, 2015
    • Bioinformatics for Cancer Genomics: Toronto, May 25-29, 2015
    • Pathway and Network Analysis of –omics Data: Toronto, June 1-3, 2015
    • Microarray Expression Analysis: Toronto, June 4-5, 2015
    • Informatics for RNA-Seq Analysis: Toronto, June 8-9, 2015
    • Informatics on High-Throughput Sequencing Data:  Toronto, June 10-11, 2015
    • Informatics and Statistics for Metabolomics: Montreal, June 15-16, 2015
    • (NEW) Analysis of Metagenomic Data: Halifax, June 24-26, 2015

    A link to the full program poster can be found at: http://bioinformatics.ca/workshops/2015.

    ELIXIR UK are seeking a Software Developer

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    Software Developer

    Oxford e-Research Centre, Oxford

    In this varied, interesting and challenging role the successful candidate will provide technical knowledge, software engineering and leadership ability for (i) a growing portfolio of data and knowledge management projects funded by UK, EU and NIH, and (ii) activities for the ELIXIR UK node of the ELIXIR programme.

    More Details are available here

    ELIXIR-UK attended the ELIXIR Innovation and SME forum in Copenhagen

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    Chris Ponting attended the ELIXIR Innovation and SME forum on behalf of ELIXIR-UK. The meeting was arranged by the ELIXIR Danish Node and ELIXIR Hub, held Monday, 24 November  - Tuesday, 25 November 2014.
    This was an interactive two-day ELIXIR Innovation and SME forum on ELIXIR’s services and activities relevant to industry. The forum will provided the opportunity to introduce some of the tools, data resources and services that are available through ELIXIR, allowing industry attendees chance to integrate these resources into their businesses planning. The forum also provided opportunity to network with other SMEs, meet local ELIXIR representatives and find out about important future developments within this key infrastructure for biological data.
    The content of the forum was specifically selected to provide the most relevant information for SME needs, and included sessions on:•Local ELIXIR services run by the Danish ELIXIR Node and services of other ELIXIR Nodes;•Opportunities for collaboration with academia through Horizon 2020;•ELIXIR’s future HPC/Cloud provisions; and•Tech Track sessions on tools and resources from ELIXIR Nodes.

    Seminar introducing in silico drug discovery/design given at Bangor University

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    Lee Larcombe delivered a seminar to MSc students at Bangor University on Nov 13th 2014, introducing in silico concepts for the design and development of drugs. This seminar aims to provide a basic understanding of the concept of protein and molecular in silico engineering/design as part of the drug development process:- Introducing theory and approaches, drivers, databases and software – and with a focus on safety and efficacy.

    TGAC and Software Carpentry Train the Trainer event

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    On 22nd and 23rd October The Genome Analysis Centre (TGAC) hosted the Software Carpentry face-to-face Instructors Training. The course was taught by Greg Wilson, the founder of Software Carpentry and Bill Mills, the Mozilla Science Lab Community Manager. For two days 39 people learnt how to effectively teach essential lab skills for computational science.

    This intense course covered a number of topics: from modern teaching methods such as lesson planning and peer instruction to the particularities of Software and Data Carpentry training infrastructure. Collaborative development of training materials was also discussed.

    The event helps to grow the pool of certified instructors who can deliver Software and Data Carpentry training across Europe. Software and Data Carpentry workshops have received very positive reception among many life science researchers. ELIXIR UK is supporting the development of both initiatives within other ELIXIR Nodes. The activities are led by the two ELIXIR UK Training sectors: Data Curation & Standards and ICT & Software.

    ELIXIR UK update at the ELIXIR Board

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    The ELIXIR Board meeting was held in Hinxton, Cambridge on the 3rd and 4th of November 2014. ELIXIR UK presented an update of Node activities - the slides are available on SlideShare, linked below:

     

    Second ELIXIR UK update meeting

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    The meeting involved representatives from across ELIXIR UK sector activities, the core Node operations group, the Node Scientific Advisory Committee and members of the ELIXIR Hub. Updates were presented on the progress of the Node to date, key achievements, and vision moving forward. ELIXIR UK will focus on training to address strategic needs in: Clinical Genomics; Applied Genomics; Structural Bioinformatics; Metabolomics; and Advanced Scientific Skills.

    Slides presented at this meeting are available on SlideShare here

    ELIXIR UK to provide Software Carpentry for MSc Clinical Bioinformatics students

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    In collaboration with Professor Andy Brass from the University of Manchester, ELIXIR UK has integrated a Software Carpentry workshop within the NHS Clinical Bioinformatics curriculum.

    This Software Carpentry workshop (lasting 3 days: 10-12th November) is  part of the 5-day MSc Clinical Bioinformatics programme (10-14th November). During the hands-on training sessions we will cover core skills such as effectively working with command line, structured software development and version control. The participants will be encouraged to help one another and to apply what they have learned to their own research problems.

    Software Carpentry is a partner of ELIXIR UK.

     

    CGAT Genomics Training Fellow (2 posts)

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    Professor Chris Ponting was initially awarded 5 years’ funding to establish a Strategic Programme in Computational Genomics Analysis and Training (CGAT;www.cgat.org) within the MRC Functional Genomics Unit in Oxford. CGAT has been training eight postdoctoral scientists in computational genomics thereby providing expertise and added value to other UK-wide institutions. Funding for this programme has recently been extended and we are seeking to recruit two further scientists. Each Fellow will be assigned to diverse genomics projects that all focus on the analysis and biological interpretation of next-generation sequence data. Projects are collaborative involving scientists from across the UK. Training will be provided through close coaching by a senior CGAT scientist, as well as through tailored courses and tutorials.

    A PhD/DPhil in biology, medical biology or a field relevant to computational genomics is essential. Excellent organisational and communication skills are required, together with the ability to work well independently and within a team. A willingness and ability to learn advanced computational and statistical skills, as well as good familiarity with computers and office software are required.

    The closing date for applications is 12.00 midday on Friday 5 December 2014.

    Further details here

    Announcing the first Data Carpentry workshop in the UK

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    The workshop is aimed at researchers in life sciences at all levels, including postgraduate students. Data Carpentry is designed to teach basic concepts, skills and tools for working more effectively with data.

    The workshop will cover the following topics:

    • How to use spreadsheet programs (such as Excel) more effectively, and the limitations of such programs.
    • Getting data out of spreadsheets and into more powerful tools (R/Python).
    • Using databases, including managing and querying data in SQL.
    • Workflows and automating repetitive tasks, in particular using the command line shell.

     

    Data Carpentry is a partner of ELIXIR UK.

     

    ELIXIR UK represented at HubBub Conference

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    The Conference had a range of prolific speakers who explained their motivations for using the software, the new features and tools they have developed for it, and the trials and successes they faced. 
    The last day of the HubBub conference was the HubHero Hackathon where a group of twenty or so hackers got together to create and contribute a range of new plug-ins, modules and components for the HubZero platform. Niall spent his time writing a component to export publicly available tutorials and course materials into the common exchange format - XML. He did this in an older version of HubZero so that existing HubZero deployments could add the component and have their content aggregated into TeSS.

    "Advanced R" Software Carpentry bootcamp at UZH/ETHZ in Zurich

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    The workshop is sponsored by the RADIANT consortium. The lecturers, Laurent and Robert, work in Bioinformatics, but the course content is intended to be quite general. It is intended for people who are already competent in R, but need/want to get some more advanced topics (e.g. package building). The workshop is planned for about 30 participants.

    THE EXACT MATERIAL WILL INCLUDE:

    • MAKEFILES AND AUTOMATION;
    • PACKAGE DEVELOPMENT;
    • FUNCTIONAL PROGRAMMING;
    • REPRODUCIBLE RESEARCH;
    • ROXYGEN FOR DOCUMENTATION;
    • RCPP + BIOCPARALLEL + GITHUB.

    HEE Genomics Education Programme website is now live

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    on behalf of the Genomics Education Programme Team

    We are delighted to let you know that the HEE Genomics Education Programme website is now live at www.genomicseducation.org.uk.

    The website is the digital home of the Programme’s activities and over time will provide online education and training in genomics for all staff in the NHS.

    At launch, the site hosts:

    • an introductory video on genomics, presented by science writer and broadcaster Vivienne Parry;
    • two new online courses for healthcare professionals: ‘Introduction to Genomics’ and ‘Introduction to Bioinformatics’; and
    • the Programme’s blog: ‘New in genomics’

    Plans to expand the website include:

    • learning and teaching resources on genomic medicine;
    • continuing professional development courses for a range of healthcare professions; and
    • details about the forthcoming Masters degree in Genomic Medicine, a multi-professional programme fully funded by HEE as part of the Programme.

    For more information about the Genomics Education Programme, visit: www.genomicseducation.org.uk/about

    ELIXIR UK Kick-Off Meeting. Manchester, UK

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    Members of the ELIXIR UK node met in Manchester on the 28th of July to review progress to date, discuss training activities and plan future strategy for the node. This landmark meeting brought together all the stakeholders and interested parties in ELIXIR UK for the first time, and marked a formal beginning of coordinated node activities.

    ELIXIR-UK Runs ELIXIR Instructor Training in Lausanne, Switzerland, 13-14 January 2016

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    The event in Lausanne concluded a series of pilot activities which started a year ago and focused on introducing Data and Software Carpentry workshops. The first event was hosted by ELIXIR Finland and included a Data Carpentry introduction and hackathon for creating materials and a Data Carpentry workshop. The second event of similar structure (a hackathon and a workshop) was held by ELIXIR Netherlands. Thanks to this earlier outreach most participants in Lausanne already had exposure to how the workshops are run.

    Almost all attendees are strongly engaged in developing and delivering teaching at their home institutions and the Instructor Training was a great opportunity to discuss best practices in teaching. The first day of the Instructor Training in Lausanne focused on a number of topics in educational psychology. The discussions on the second day covered matters more specific to Data and Software Carpentry workshops.

    The leaders of the ELIXIR Train the Trainer (TtT) task are interested in a possibility of incorporating the Software and Data Carpentry Instructor Training programme in the TtT package. The Institute will be happy to facilitate this collaboration.

    Training details: http://swcarpentry.github.io/2016-01-13-instructor-training-lausanne/

    ELIXIR Estonia provided a half-a-day course for researchers working with high-throughput (expression) data at the University of Oxford.

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    ELIXIR trainers from Estonia visited researchers in Oxford and introduced web-based tools to analyse and interpret high-throughput biological data. The main focus was g:Profiler - a toolset for finding the most significant functional groups for a given gene or protein list; MEM - a query engine allowing users to mine hundreds of public gene expression datasets to find most co-expressed genes based on a query gene; and ClustVis - a web tool for visualising clustering of multivariate data using Principal Component Analysis plots and heatmaps.

    This course was oversubscribed and has received great feedback from the participants.

     

    Software/Data Carpentry Instructor Training for ELIXIR Trainers in Manchester 22-23 November Was a Great Success

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    Software/Data Carpentry Instructor Training workshop for ELIXIR trainers organised by ELIXIR-UK in Manchester 22-23 November was a great success.

    The workshop was run by Greg Wilson from Software Carpentry Foundation, Aleksandra Pawlik from SSI and Karin Lagesen from University of Oslo.

    In the process, we trained 24 new Software/Data Carpentry instructors from a number of ELIXIR nodes (UK, Netherlands, Norway, Slovenia, Spain, France). In addition, Aleksandra Pawlik and Karin Lagesen both got certified to run Software/Data Carpentry instructor training workshops independently - they are the first such instructors from Europe, which will make it easier for us to run such workshops in the future.

    Some comments from the participants of the workshop:

    "Greg - you were inspiring. It went very well indeed. And thanks for the great ideas."

    "I'll be offline again today, too much good stuff happening in the train the trainer. This course is brilliant."

    "Very many thanks for the software / data carpentry instructors training this week. I learned a lot from it - not least because you all were so enthusiastic about learning how to share what you know."

    ELIXIR UK and Slovenia organise the first Data Carpentry workshop in Ljubljana

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    ELIXIR UK and ELIXIR Slovenia organised the first Data Carpentry workshop in Ljubljana, Slovenia on 20-21 July 2015.

    The workshop was hosted by the Faculty of Medicine, University of Ljubljana and National Institute of Biology, Ljubljana, and carried our by ELIXIR UK. The places for the workshop were gone within the days of announcing it and the comments from trainees were extremely positive.

    ELIXIR UK is looking forward to co-organising more Software and Data Carpentry events with our Slovenian partners.

    Data Carpentry hackathon and workshop at ELIXIR Netherlands

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    The hackathon consisted of two days during which the participants representing 10 ELIXIR Nodes worked on Data Carpentry training materials. The first day started with the introduction to Data and Software Carpentry teaching model. This was then followed by a review and discussion on the existing materials. The participants made suggestions about the possible improvements for the existing materials and new topics to be developed. The overall theme of the hackathon was "genomics" and hence the participants could base their work on the existing contents for teaching genomics in Data Carpentry. Eventually three groups were formed:

    • Group 1 which worked on creating training materials on using ELIXIR Cloud resources.
    • Group 2 which worked on a decision tree for using cloud computing.
    • Group 3 which worked on different aspects of understanding how to use one's data for genomics. In particular the group worked on describing the file formats, file manipulation, pipelines integration, post-assembly - de novo RNA Transcriptome Analysis, handling blast annotation output and verifying data.

    The hackathon was facilitated by Karthik Ram (University of Berkeley, rOpenSci, Data Carpentry) and Aleksandra Pawlik (University of Manchester, Software Sustainability Institute). After the hackathon Karthik and Aleksandra then taught a 2-day Data Carpentry workshop. It was the first Data Carpentry workshop in Netherlands. 30 students registered to attend it. All of them were from life science research area. The workshop covered the standard Data Carpentry curriculum. One module was added at the end of the second day. This module covered using ELIXIR Cloud resources and was the first time the materials created during the hackathon were used for actual teaching.

    The whole event received positive feedback and on the overall this Pilot Project appears to have a great reception within ELIXIR. The Slovenian and Belgian Node are running workshops this year and it is likely that other will follow soon.

    Data Carpentry hackathon and workshop at ELIXIR Finland

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    The event consisted of two parts. The first part was a two-day hackathon to create new and improve existing training materials for Data Carpentry. Another purpose of the hackathon was to introduce the concept, paradigms and models of teaching for Software and Data Carpentry to the representatives of the ELIXIR Nodes. As 11 Nodes were represented at the hackathon, the goal of spreading the knowledge about the Carpentry model of training to be then used to support ELIXIR training activities was achieved. The attendees of the workshop were Mateusz Kuzak and Philip Lijnzaad (representing ELIXIR NL), Diana Marek (ELIXIR CH), Hedi Peterson (ELIXIR EE), Damiano Piovesan, Andrea Manconi and Angel Corpuz (ELIXIR IT), Francois Sabot (ELIXIR FR), Gonçalo Antunes (ELIXIR PT), Vojtech Spiwok (ELIXIR CZ), Frederik Coppens (ELIXIR BE), Peter Juvan (ELIXIR SI), Maria Lehtivaara and Joona Lehtomäki (ELIXIR FI), Aleksandra Pawlik (ELIXIR UK).

     
    The event was run by François Michonneau of the University of Florida who is an experienced Data Carpentry instructor and training materials contributor, and Aleksandra Pawlik from the Software Sustainability Institute at University of Manchester, who is also a member of both Software and Data Carpentry Steering Committees.
     
    The first day of the hackathon started with introductory presentation about Data Carpentry given by Aleksandra. Then François provided a walk through the Software and Data Carpentry lesson template and discussed the licensing of the training materials. This was then followed by a discussion about collaborative lesson development which is one of the foundations of Software and Data Carpentry. It also provided an opportunity to look at the proposed ideas for the hackathon. The attendees could select to work on the suggested topics or introduce their own.
     
    The further work during the hackathon the carried on in different teams who focused on developing new material or improving and enhancing the existing one. The projects covered during the hackathon included:
    • development of the dplyr module for the R lessons;
    • development of NGS data analysis lessons;
    • development of RNAseq data analysis using BRB Digital Gene Expression;
    • improvements on the shell lessons;
    • improvement of the spreadsheet lessons.
     
    The hackathon was followed by a Data Carpentry workshop also hosted at the CSC IT Center for Science. The participants of the workshop were mainly based in Finland however there were a few researchers from Estonia. We started the workshop with the spreadsheet lessons which then were followed by the introduction to R. The second day of the workshop started with shell lessons. The participants had very diverse background - some never prorgammed and some had significant experience in writing source code. Delivering the shell lesson was also a challenge because the skills related to using command line also varied. The next part of the workshop covered structured data with SQL. The second day finished with the newly developed 'dplyr' module and some more advanced R features.
     
    It was intense four days filled in with discussions, hands-on teaching and learning, knowledge sharing and discussing the usability of the Carpentry model for training in ELIXIR. The next event within the pilot project will be hosted by the Dutch Node on 22-25 June 2015 at the Utrecht University.
     
    The hackathon and workshop in Finland would not have been possible with a lot of engagement, effort and help from the hosts: Tommi Nyrönen, Eija Korpelainen  and Ari-Matti Saren.

    Newly certified ELIXIR Software and Data Carpentry Instructors

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    The newly certified ELIXIR Software and Data Carpentry Instructors are (in alphabetical order):

    • Vincenza Colonna  (ELIXIR Italy)
    • Dmytro Fishman (ELIXIR Estonia)
    • Matthias Haeni (ELIXIR Switzerland)
    • Frank Pennekamp (ELIXIR Switzerland)
    • Elena Sugis (ELIXIR Estonia)
    • Allegra Via (ELIXIR Italy)

    The remaining 14 attendees are scheduled to be certified (pending a completion of the Instructor Checkout Procedure) in the coming weeks. We are really excited to see the pool of Software and Data Carpentry Instructors grow within ELIXIR and hope that this will help scale up and coordinate training activities across the Nodes.