EMBL Bio-IT Hackathon 2019

4 July 2019

09:30-17:00. Room 13.518, EMBL Heidelberg

This year, as well as the annual “Thank You” BBQ, EMBL Bio-IT will be hosting its first Hackathon! This will be a chance for all our community members to work together to develop new and existing tools, resources, and material for EMBL’s computational biology and bioinformatics community.

  • The day will begin with lightning talks to introduce the projects and goals for the day, followed by dividing into project teams.
  • Food and hot drinks will be provided all day
  • At 16:15, we will conclude with a brief summary from each team, showcasing what they’ve achieved and suggesting next steps for the project.
  • The Bio-IT “Thank You” BBQ will begin at 17:00.

Projects

Projects for the Hackathon, proposed by Bio-IT community members, are listed below. Click on the relevant title to expand more details about each project.

Got an idea for anothe project for the Hackathon? There’s still time to add it to the list! To submit a project idea, contact us at bio-it@embl.de.

Developing an interactive dashboard for cluster usage analysis

Project Summary

We’d like to make it easier for users of the EMBL compute cluster to access easy-to-understand summaries of their cluster usage and guidance for how they might improve the efficiency of their compute tasks. This will be achieved by developing an R-Shiny interface to the cluster Slurm database, which will allow EMBL users to view summary visualisations and statistics on their cluster jobs and receive advice on how they might improve the performance of their jobs in the future.

What do you hope to achieve during the Hackathon?
  • expand on work started by Mike Smith towards this goal
  • connect to the Slurm database and extract relevant data for analysis/plotting
  • analyse and visualise data retrieved from the database
  • create a Shiny interface to these functions/analyses
What skills should people have to be able to contribute to the project?
  • basic R skills
  • experience with and/or interest in any/all of databases, cluster usage, data analysis/visualisation, and R-Shiny would be beneficial
Can you link to/provide information that contributors can/should read before the Hackathon?
  • Mike’s job summary interface: https://spinoza.embl.de/shiny/msmith/slurm-job-summary/
  • and source code: https://git.embl.de/msmith/slurm_dashboard
  • EMBL cluster wiki: https://wiki.embl.de/cluster/Main_Page
Contribute to this project if you’re interested in…
  • data analysis and visualisation
  • R-Shiny
  • working with data in (large) databases
  • cluster usage
  • encouraging better compute practices at EMBL
Contact person/people

Jure Pečar (pecar@embl.de)

Developing an app for EMBL clubs

Project Summary

There are a lot of clubs at EMBL, and many of these share some common challenges e.g. scheduling meetings, games, etc and finding out who’s planning to attend. This project team would develop an app to help clubs coordinate their activities.

What do you hope to achieve during the Hackathon?

Create an app that allows users to add club members, communicate with them, poll their availability, etc.

What skills should people have to be able to contribute to the project?
  • Ivan doesn’t have much mobile app development experience, so anyone with experience (even if you can’t attend the hackathon!), please contact him (email below)
Can you link to/provide information that contributors can/should read before the Hackathon?
Contribute to this project if you’re interested in…
  • getting some experience with app development
  • helping EMBL clubs
Contact person/people

Ivan Berest (ivan.berest@embl.de)

Creating a directory of methods and tools used by EMBL groups

Project Summary

There is a great diversity of different research topics and methodologies spread across the six EMBL sites. When a researcher is getting started with a new approach and/or field, it would be helpful to be able to quickly find out who else at EMBL has experience with this. This project team would work to create a searchable directory of techniques/methods/analyses used by research groups across EMBL.

What do you hope to achieve during the Hackathon?
  • collect information about methods used and areas of interest for EMBL groups (e.g. based on group webpages and recent publications)
  • organise this information in a database
  • create an interface allowing users to search/filter this database
What skills should people have to be able to contribute to the project?
  • text mining and/or web scraping experience would be highly beneficial
  • experience with creating databases and front-end interfaces would also be valuable
Can you link to/provide information that contributors can/should read before the Hackathon?
Contribute to this project if you’re interested in…
  • helping connect EMBL researchers and build collaborations
Contact person/people

Ivan Berest (ivan.berest@embl.de)

Developing Bio-IT version control training material

Project Summary

We’d like to build on the excellent training material on Version Control with Git, originally developed by Genome Biology Computational Support (GBCS), incorporating some of the examples and material from recent Bio-IT courses on the topic.

What do you hope to achieve during the Hackathon?
  • Add extra material to a fork of the GBCS material linked above, e.g.
    • reverting changes
    • branching and merging
    • setting up continuous integration
    • GitLab Pages
What skills should people have to be able to contribute to the project?
  • basic experience with Git and GitLab
  • familiarity with Markdown would be beneficial
Can you link to/provide information that contributors can/should read before the Hackathon?
  • GBCS Git training material: https://gbservices.embl.de/git-conda/
  • Bio-IT repositories for previous Git training (for reference, no need to read ahead!):
    • beginner: https://git.embl.de/grp-bio-it/linuxcommandline/tree/master/git_beginner
    • intermediate: https://git.embl.de/grp-bio-it/intermediate-git
    • CI/Pages: https://git.embl.de/stamper/horsing-around/
Contribute to this project if you’re interested in…
  • developing high-quality teaching material
  • helping spread good software development practices at EMBL
  • gaining experience with GitLab/GitHub/authoring and publishing static web pages
Contact person/people

Toby Hodges (toby.hodges@embl.de)

EMBL image analysis training resource

Project Summary

The project team would add to and improve the Image Analysis Training Resources project currently under development at https://git.embl.de/grp-bio-it/image-analysis-training-resources. These resources aim to provide a single interface for people to teach/learn important concepts in image analysis, regardless of the platform with which they want to do their image analysis (ImageJ/Fiji, Python, MATLAB, etc).

What do you hope to achieve during the Hackathon?

During the Hackathon, this project team will contribute to the existing material by, for example:

  • adding new modules for concepts that aren’t yet covered
  • adding example code and exercises to existing modules/lessons
  • creating new/converting existing graph visualisations so that they render in all modern web browsers
  • any other improvements that you might want to make!
What skills should people have to be able to contribute to the project?
  • familiarity with Markdown and the GitLab interface essential
  • experience with image analysis and/or Jekyll/static site generators would be helpful, but not essential
Can you link to/provide information that contributors can/should read before the Hackathon?

To get started quickly, project participants should have looked through the associated GitLab repository: https://git.embl.de/grp-bio-it/image-analysis-training-resources. Please feel free to contact me beforehand if you have any questions (see email below).

Contribute to this project if you’re interested in…
  • contributing to teaching material/an open source project
  • learning about how GitLab Pages/Jekyll works to create websites from text files
  • helping people learn how to analyse image data
Contact person/people

Toby Hodges (toby.hodges@embl.de)

Teach an advanced data skill: Create short tutorials on advanced Python, R, or other approaches

Project Summary

Bio-IT has been offering many beginners lessons on computing skills such as Python, R, Unix, git, etc. Our learners who finish these courses seek new and advanced skills that they can learn and apply in their work. With this project idea, I would like to invite the bioinformaticians to share one of their favorite skills by creating a small tutorial that can be taught by someone, or can be used for self-paced training.

What do you hope to achieve during the Hackathon?
  • Short tutorial on skills for data analysis using techniques such as Machine Learning, statistical analysis, visualization, etc.
  • The tutorial should include the objective of the material, introduction to the concept, code snippets, examples, optional exercises and set of references that one can use to get more information.
  • The tutorial developed at the hackathon will be hosted on the git.embl.de using Open Source License.
What skills should people have to be able to contribute to the project?
  • Exeperience with one or multiple data science techniques or programming language.
Can you link to/provide information that contributors can/should read before the Hackathon?
Contribute to this project if you’re interested in…
  • sharing a programming or computing skills.
  • Creating online learning resource.
Contact person/people
  • Malvika Sharan (malvika.sharan@embl.de)

Creating stories from community interviews

Project Summary

Malvika has been interviewing members of the Bio-IT community over the past six months, talking about their career paths in computational biology/bioinformatics. Now that all of these interviews have been transcribed, we’d like to summarise them into stories where shared narratives exist and highlighting common advice that interviewees had for people in computational career paths.

What do you hope to achieve during the Hackathon?
  • review the transcripts and agree on topics for some blogposts that could be made from the material
  • begin drafting some of these blogposts
What skills should people have to be able to contribute to the project?
  • anyone is welcome to contribute
Can you link to/provide information that contributors can/should read before the Hackathon?
  • contact me for access to the transcripts and data that we will work from at the Hackathon (see email details below)
Contribute to this project if you’re interested in…
  • storytelling
  • creative writing
  • blogging
Contact person/people

Malvika Sharan (malvika.sharan@embl.de)

Creating content to expand resources.embl.org

Project Summary

Community-driven open source visual library of icons for scientific figures, graphical abstracts and presentations

Scientific figures, graphical abstracts, presentations. They’re all based on icons scientists spend hours on drawing or dealing with copyrights issues. How about saving researchers these hours by bringing EMBL community together, and a creating a visual library of high quality icons available in .eps format? Icons that once created, can be reused, modified and recycled again and again by anyone? This resource would include icons starting from simple objects through DNA strands, organelles and model organisms, to lab equipment, and much more!

What do you hope to achieve during the Hackathon?
  • Creating icons together
  • Share, annotate, improve existing icons and images
What skills should people have to be able to contribute to the project?
Can you link to/provide information that contributors can/should read before the Hackathon?
Contribute to this project if you’re interested in…
  • making it easier for EMBL scientists to use high-quality images in presentations etc
  • making EMBL more recognisable because of a shared “look & feel” of graphics used
Contact person/people
  • Tabea Rauscher (Design Team Lead, tabea.rauscher@embl.de)
  • Aleksandra Krolik (aleksandra.krolik@embl.de)

Go to the registration page to join a team that will work on one of the projects above during the Hackathon.

Get Involved

Pitch a project

Recruit other community members to a team to work on your project idea.

Projects pitched for the Hackathon could be related (but not limited) to one of the following ideas:

  • Improving existing computing resources supported, maintained or hosted by Bio-IT
  • Creating a new resource or tool for the community
  • Creating documentation e.g. a ‘how-to’ guide for the existing resources
  • A tutorial that others in the community might be able to use
  • Creating a workshop material for your resources that can be offered through Bio-IT
  • Writing a blog for Bio-IT Blog platform
  • Creating handout, guidelines, or other material to help users use your materials or teach them to others
  • Reporting bugs or fixing issues in the existing materials or tool that would be useful for the Bio-IT community
  • Creating a list of resources, things etc. that we lack in the community and could be developed in coming years

Can’t make it for the call? Don’t worry if you can’t join the project pitching call on June 4th - you can also submit a project idea by creating an Issue on this repository or by sending us an email. You can do this any time up to Monday 1 July 2019.

When designing your project, you might want to consider the following things:

  • what is the problem you’re trying to solve/the end-product you’re trying to create?
  • what do you hope to have achieved by the end of the hackathon? Be realistic! The Hackathon will last just under seven hours - what tasks do you think could be completed in that time? (It’s ok if your project isn’t finished in the one day, but there should be some achievable targets for the hackathon itself.)
  • can this be divided into multiple tasks? If you will have a team of multiple people, how could the project be divided among them? Will you pair people up to work on the objectives together? All work as one team? Work individually?
  • can you link to material that people should read before and/or refer to during the hackathon?
  • what will people need to know before they start? For example, would one need to be an expert R user to contribute? What packages/modules/tools should people be familiar with before the Hackathon begins?

Join a project team

You don’t need to have your own project idea to join the Hackathon. Take a look through the list of projects and choose one that’s interesting to you. Then sign up to contribute to that project by registering on this page.

Contact

If you have any questions about the Hackathon, or anything else Bio-IT-related, please contact bio-it@embl.de.

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