Notes: Bioinformatics Open Source Conference 2016 day 1 afternoon: Standards; Panel on growing communities

I’m at the 2016 Bioinformatics Open Source Conference (BOSC) in Orlando and these are the notes from the afternoon sessions from the first day focusing on standards and a panel on growing and sustaining open source communities.

Other notes:

  • Day 1 morning notes – Jennifer Gardy keynote on open data and infectious diseases, plus workflow development


Andre Masella – Enhancements to MISO: An open-source community-driven LIMS

Andre describes the use of MISO LIMS at OICR integrating with SeqWare. Cool because a different workflow system than development team at TGAC/Earlham Institute. 1 developer at Earlham and 4 developers at OICR. Require code reviews for everything with at least two developers – have a mainline with site-specific repositories for configuration. Nice development processes. Lots of configurable plug ins to externalize the configuration so handles lots of new integration features. Planning to expand the tissue processing workflow used at OICR. Also planning to continue to improve UI with new Excel-like handsontable interface.

Chunlei Wu – Biothings APIs: high-performance bioentity-centric web services

Building a unified API for biological entities. Represent heterogeneous data in a document database – JSON documents with nested key/value pairs. and – great resources for querying and retrieving information about genes and variants. Easy to use for developers – two endpoints, no API keys or sign ins. Python and R clients available for usage. Incredible update rate: weekly for genes, monthly for variants. is an great resource for the community. Scales to 5M hits/day with 99.9%+ availability and quick return times. Used by MyGene CIViC, jBrowse

Seth Carbon – The Noctua Modeling Tool

Noctua provides collaborative editing of RDF instance graphs for modeling biological processes (models). Use a LEGO abstraction for modeling biology and under the covers uses OWL for modeling LEGO. Noctua is really an abstract graph editor. It avoids pitfalls of tabular models that causes issues. By being highly collaborative you can work together at the same time remotely. Nice demo of using Noctua for chaining together complicated biological interactions: feedback loops with positive and negative feedback.

Chris Mungall – Processing phenotype data using Phenopackets-API and PXFTools

Chris emphasizes that standards enable computation, but for phenotypic information a big lack of standards compared to genomics (GFF, VCF, BED). Phenotypes are hard, so walks us through important example using Mickey Mouse. Hard to capture in words how perfect and funny this is. In seriousness, there is a lot of squishiness in defining things and we can improve this using ontologies. Shows how hard this is – in many cases need to combine multiple terms to describe. To try and improve this situation developed PXF: Phenotype Exchange Format. Handles much of the complexity required in real life descriptions. PXFTools makes it easier to work with these formats. Can use JSON-LD/RDF magic that I don’t understand to convert into triples for modeling and query. Has a reference API in Java, plus Python and Javascript bindings.

John Bradley – Towards traceable, scriptable, and efficient data distribution for next-generation genomics

John talks about the data lifecycle in research – wants to have reproducibility, provenance and versioning. Typically we have terrible ID management based on filesystems. Duke Data Service handles better provenance and management. Have a full workflow around this. Cool, similar ideas to Arvados.

Panel: Growing and sustaining open source communities

This is the always great BOSC discussion panel. The goal of this panel is to discuss how open source communities can grow and develop. We have five great panelists:

  • Natasha Wood – Establishing a bioinformatics community in western cape of South Africa using Bioinformatics unseminars.
  • Bastian Greshake – Created openSNP, a crowdsourced environment to share genomic data. Growing quickly with lots of users and 5-10 contributors on coding side.
  • Abby Cabunoc Mayes – Developer for the Mozilla Science Lab, engaging external researchers. To build a community, you need to make things.
  • John Chilton – Developer in the Galaxy project. It exists for the community and has a strong focus on users and researchers. Awesome 200 person Galaxy conference showing the strong devoted community.
  • Jamie Whitacre – Background in software development at Smithsonian, now technical project manager for Jupyter (IPython) project. Core team of 25 developers.

Discussion questions:

What is the motivation for community development? Natasha – knowing people from a large number of backgrounds helps with getting things done. Networking helps everyone. Abby – initial motivation for most people is selfish. Have to offer something useful, then they start to care about the bigger mission. Jamie and John – Galaxy origins: very bare bones initially, but got using it as more useful. For IPython, early small project that expanded as it got picked up. Bastian – different situation because people

Project solving a need, but how to define that need and differentiate to grow the community? Abby – learn things from startups. Very clear about value proposition and understanding what makes them unique. People come because they care about your mission so you have to be clear about that. John – easy to be technically focused but need to stay focused on use cases, and helping people. Jamie – having a really good idea and a strong personality. Fernando helps draw people to the project and picks a great team.

What is the value of empathy in the community building process? Jamie – recommends Art of Community to learn better about what your community needs. John – need to understand what people want key to bringing people in. Example from Galaxy: fully opened up the development process and gave the community a voice.

Building bridges between communities and maintaining identity and ownership. Abby – difficult problem, unfortunate about Mozilla Persona. OpenID. Jamie – Jupyter hub wants to maintain a single identity so people can take research and work with them.

How to foster volunteers to continue to develop within established projects that are often engrained? Abby – being able to delegate tasks. Leave small tasks for others to get do as well. As a leader, don’t do too much. Idea: have easier bugs that you can mentor people through. John – seconds Abby’s comments. In additional, breaking project into smaller units allows them to have ownership of specific components. This ownership provides incentives for people to contribute. Abby – make people feel appreciated and show what they accomplished.

How can you convert non-initiated people into your project? Abby – okay if everyone not intimately involved, can get good feedback from closely associated paper.

What about contributor badges for community contributions? Abby – a great idea. Badges show what people actually accomplished, uniquely identified with ORCiD. John – names, names, names. Highlight what people did in release notes to show you value their contributions.

What is the best strategy for dissemination and growth? Natasha – get people involved in a project. Hackathons worked. Not worked: get non-bioinformaticians involved as they are looking for bioinformaticians not wanting to get involved. Jamie – Jupyter gets best developers through long tail of interested contributors. Lots of ways to communicate and get involved with discussions. Newsletter and mailing list. They also attend a lot of events and host specific events. John – full time people doing outreach and help (Dave, Jennifer). Put in the effort to get the word out. Abby – want things to be more open by focusing on face to face and events. Mozilla Global Sprint good example of later. Study groups meet in different cities around the world.

Advice on people starting a project with a couple of developers; pitfalls? Abby – be open so everyone knows what is happening, don’t forget about rest of world. Bastian – patience, it can take time before something comes. Natasha – useful to have a clear exit strategy for people who want to be part time contributors. John – build a community by becoming part of a larger community. A lot benefit from using other projects instead of developing your own things. This helps find commonalities and collaborations.

When is a project large enough to recruit people to do community development? John – Dave Clements early on, 7th employee of Galaxy. Abby – even one person can do this. Michael – CWL, first person.

Hilmar Lapp – Open Bioinformatics Foundation (OBF) update

Hilmar starts by taking a poll of audience to see who is at BOSC for the first time. ~50% of audience – awesome to have some many new people. Provides an overview of all the work OBF does. Describes some difficult things currently affecting the community: running infrastructure with volunteers is hard. Easier to setup than to maintain over time. Open Bioinformatics involved in Google Summer of Code thanks to Kai Blin, the organization admin: 8 projects, none are original Bio* project showing the cool growth of the community. This year we have an OBF Travel Fellowship to improve diversity in the community. 3 travel awards from April 15th round, applications for August 15t rounds are now open.


2 thoughts on “Notes: Bioinformatics Open Source Conference 2016 day 1 afternoon: Standards; Panel on growing communities

  1. Pingback: Notes: Bioinformatics Open Source Conference 2016 day 2 morning: Open research and data science | Small Change Bioinformatics

  2. Pingback: Notes: Bioinformatics Open Source Conference 2016 day 2 afternoon: developer tools and reproducible analyses | Small Change Bioinformatics

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