Notes: Bioinformatics Open Source Conference 2015 day 1 afternoon — Standards, Interoperability and Diversity Panel

I’m at the 2015 Bioinformatics Open Source Conference (BOSC) in Dublin, Ireland. BOSC is a two day community conference devoted to open source and open science. These are my notes on the day 1 afternoon session on standards and interoperability, and the panel on improving diversity in the BOSC community.

Standards and Interoperability

Portable workflow and tool descriptions with the CWL

Michael R. Crusoe

Michael providing an overview of the Common Workflow Language, which is a great standard developed out of Codefest 2014 and the BOSC community. It provides a way to define workflows and tools in a re-usable and interoperable way. Looked at many existing standards and approaches. Giving a showout to Worflow4Ever which was an awesome standard to build off.

From peer-reviewed to peer-reproduced: a role for research objects in scholarly publishing in the life sciences

Alejandra Gonzalez-Beltran

Alejandra talking about research objects and the ability to use them to improve reproducibility. Work is published in PLOS-One and builds off ISATools, Galaxy and GigaScience. Took an article on SOAPdenovo2 and built up the infrastructure that should have been present: description of the experimental steps in ISATab, running in Galaxy. Publishing findings as nanopublications in RDF and linked the statements of results with experimental descriptions. The idea behind Research Objects is that they bring together data, analysis and conclusions.

Demystifying the Interoperability of Disparate Genomic Resources

Daniel Blankenberg

Dan starts by describing what Galaxy is, trying to correct some earlier misconceptions and define the goals of the project. Awesome new thing is the interactive support for iPython and RStudio. Main goal of talk is talking about getting data into Galaxy in more automated ways, including multiple files and metadata and GenomeSpace. Export data out of Galaxy to places like UCSC or to other sinks like GenomeSpace. Whew, a whirlwind tour.

Increasing the utility of Galaxy workflows

John Chilton

John is talking about Galaxy workflows, designed for biologists. However only used by 15% of users, perhaps because of limitations. It previously only scheduled jobs, but now handles map/reduce system operations and has a real workflow engine. Now have Collection types (list and paired). Support for dealing with these via a nice web interface and build the sample relationships themselves. Now can do solid sample tracking and tools can consumed paired datasets. John shows some nice examples of community developed workflows. The workflow engine and model is so nice now, lots of great features. I’m looking forward to building on top of it with bcbio when everything will be CWL.

Kipper: A software package for sequence database versioning for Galaxy bioinformatics servers

Damion Dooley

Kipper focuses on helping to recreate sequencing analysis by organizing reference databases. Some of them are nice and you can get and download previous databases, but large stuff like NCBI is continuously updated. Kipper is a Python script that keeps track of everything.

Evolution of the Galaxy tool ecosystem – happier developers, happier users

Martin Čech

Martin talks about recent improvements to the tool shed to make it easier to use for developers. Galaxy involved with the ICGC-TCGA DREAM challenge for re-running. Awesome. Planemo helps in testing and developing new tools, treating Galaxy as a transparent dependency.

Bionode – Modular and universal bioinformatics

Bruno Vieira

Bionode is a javascript library for working with biological data. Works both in the browser and locally with node.js. Really nice looking code: Code in GitHub. Also takls about the really cool oSwitch to help make it easy to run local commands in Docker containers with the actual tools.

The EDAM Ontology

Hervé Ménager

EDAM Ontology describes bioinformatics operations, data types and topics. It’s a critical way to define reproducibile workfows so we know what is happening where and can convert between different tools that do the work. It’s part of ELIXIR so will be in new infrastructure.

Panel Discussion – Open Source, Open Door: Increasing diversity in the bioinformatics open source community

Mónica Muñoz-Torres, Holly Bik, Michael R. Crusoe, Aleksandra Pawlik, Jason Williams

Moni is chairing the panel, talking about our goals at BOSC to have a more diverse community. We want to welcome underrepresented members of all types, to help encirch the set of skills and opinions in our community. The experience of the panelists is so incredible: helping bring new scientists into the community from all levels. There are a large number of cultures and communities we interact with, how can we better at that.

The goal of the panel is in starting the conversation and hearing people’s voices. Goal is to hear about the situations that make people feel uncomfortable and try to remedy them. How can we set up BOSC to not make people feel excluded?

How do you start get involved with the community? Holly’s recommendation: volunteer to help with organizing. Yes please, we’d love to have more help with BOSC organizing. Conversely, how to bring more people into your community? Provide role models for the people you want to attract. Need to build and encourage diverse set of role models.

How can you get more diverse applicants? Often get a large number of men applications and very few women applicants. Suggestions: pay better, more flexibility for working hours. Paying undergraduates to work in the lab to create a more diverse environment. Co-mentoring with other groups – say more biology focused and more computational focused. Also a numbers problem: we need to be investing in education of under-represented of younger students. Can we sell and provide a clear career path for bioinformatics so people want to go into bioinformatics?

Suggestions for helping to improve diversity and open science. Collaborate with folks who don’t normally do that and bring your diverse, open worldview into the collaboration.

Bioinformatics is a chance for more people to get involved. All you need is an internet connection and community. The barrier is the knowledge. We need to motivate and welcome people to become involved, then provide the training to get them there.


2 thoughts on “Notes: Bioinformatics Open Source Conference 2015 day 1 afternoon — Standards, Interoperability and Diversity Panel

  1. Pingback: Notes: Bioinformatics Open Source Conference 2015 day 2 morning — Ewan Birney, Open Science and Reproducibility | Small Change Bioinformatics

  2. Pingback: Notes: Bioinformatics Open Source Conference 2015 day 2 afternoon: Translational, Visualization and Lightning Talks | Small Change Bioinformatics

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