Notes: Bioinformatics Open Source Conference 2016 day 2 afternoon: developer tools and reproducible analyses

I’m at the 2016 Bioinformatics Open Source Conference (BOSC) in Orlando and these are the notes from the afternoon session on the second day, focused on developer tools and libraries, approaches for improving open science and reproducibility and a set of lightning talks to wrap up the day. It was another great conference thanks to Nomi, Peter, Hilmar, Moni, Heather, Chris, Karsten and the rest of the Open Bioinformatics Community.

Other notes:

  • Day 1 morning notes – Jennifer Gardy keynote on open data and infectious diseases, plus workflow development
  • Day 1 afternoon notes – Talks on standards and a panel on growing communities.
  • Day 2 afternoon notes – Steven Salzberg keynote on open source, data and access in science plus talk session on data science.

Developer tools and libraries

Christian Brueffer – Biopython Project Update 2016

Christian talks through the history of Biopython from 1999 until today. OpenHub has some great statistics on new contributors and contributions over the past year from GitHub. There is an entire filled slide with new contributors over the last year – an amazing platform for bringing new people into the community. Some cool changes – updates to Bio.SeqIO, Bio.PDB, Bio.Restriction, Bio.Data… Amazing diversity of new changes cool to have them catalogued in a single place and highlight contributors. New things coming for Biopython 1.68: updates to Bio.pairwise2 to make it faster. Cool since one of the initial things written by Jeff Chang early in the project. Christian personally working on improving standard style in Biopython since there are widely different coding styles in the past. Now providing standard style checking through TravisCI.

Peter Humburg – ReportMD: Writing complex scientific reports in R

Provide reproducibility of data analysis through literate programming. Rmarkdown makes this easy in R but flow of analysis may limit presentation of results. Want to communicate the story without two different stories. ReportMD generates multi-page HTML and amanages dependencies between markdown files. Lots of useful flexibility in analyses.

Shaun Jackman – Linuxbrew and Homebrew-Science to Navigate the Software Dependency Labyrinth

Shaun talks about the importance of reproducibility in analyses – be able to generate the same results, both yourself and others. Installing tools to do this is a huge challenge, hence the incredible work on Linuxbrew and Homebrew science. Amazing work porting homebrew to linux and building a community to install scientific packages.

Benjamin Hitz – SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

ENCODE DCC manages data for ENCODE project, encodeD provides a flexible metadata modle for representing samples and SnoVault is a general purpose database it uses for representing it. Uses JSON-SCHEMA and JSON-LD to validate and normalize the data. Database can be exported as RDF and put into a SPARQL store and has an auditing system to check cross-object data integrity. Cool ideas, would love to understand how it compares to Datomic for representation.

Open Science and Reproducibility

Bastian Greshake – State of the Union: Dockerizing, Crowdfunding & Opening for Contributors

OpenSNP leverages the availability of direct to consumer sequencing. Allows users to directly share their data and many people willing to share phenotypes as well. Different sharing for traits (hair color) versus diseases (allergy). Can also share if you prefer vi or emacs (both, thank you Spacemacs). Lots of examples of open discussion but also danger of too much information if people don’t want to know. Some current growing issues (4500 users) – unassociated with any institution so looking for funding to support infrastructure and development. Patreon, Gratipay for community; SevenBridges helping as well. Broken up infrastructure into individual machines, managed with Docker containers deployed across machines. Lots of great community work to bring more people into the project. Three Google Summer of Code students working on project: adding fitbit support, phenotype integration, UI overhaul.

Michael Reich – The GenePattern Notebook Environment

Analysis approaches: analysis notebook environment like Jupyter allow you to describe, document and run analysis if you have programming skills. Bioinformatics Tool Aggregation Portals wrap existing tools and make them available to the non-programmer (Molbyle, Galaxy, GenePattern). GenePattern notebook environment makes Jupyter available to research users without requiring any programming. Michael switches over to demonstration of Jupyter versus GenePattern notebook for SVM training and prediction. Jupyter requires coding up pa bunch of loading while GenePattern avoids this by baking in lots of machine learning methods. Almost available and ready to go. Shows movie demo of trying to predict pediatric medulloblastoma outcome from genomic data.

Brett Beaulieu-Jones – Reproducibility in computationally intensive workflows with continuous analysis

Emphasizes that open science doesn’t equal reproducibility, since it can be so much work to reproduce other’s analysis. Data changes over time, so without version specified cannot get back what you did previously. Continuous analysis – combines Docker and Continuous Integration. Need Docker container + script to integrate with CI. Available on GitHub: Continuous analysis.

Nils Gehlenborg – Reproducible Research in the Cloud with the Refinery Platform

Refinery Project provides a set of visualization tool built around an ISA-TAB data repository. Uses Galaxy and CloudMan for analysis platforms. Runs on AWS to spin up CloudMan for analysis. Nice work to handle provenance graphs by collapsing and expansion – so can try to see the correct representation based on interest: called Avacado.

Lightning talks

Mónica Muñoz-Torres – Apollo Genome Annotation Editor: Latest Updates, Including Galaxy Integration

Apollo provides real time interactive collaborative editing. Architecture is an Apollo Server connected to clients – web clients, jBrowse. Latest news: export and update Chado databases, annotate multiple organisms per server, integration with Galaxy. Can bring in annotations from many different inputs.

Michael Zentner – An invitation to the bioinformatics community to participate in the HUBzero® open source release

HubZero is a software platform to create web sites to for scientific research and teaching. Tries to help folks provide web interfaces for tools. Organized through containers, showing examples from molecular dynamics. Looking at hosting Jupyter and arbitrary web apps. Remidi Central is a collection of 250 hospitals that share date through HubZero. Looking for partners in the bioinformatics community.

Peter Rose – PDB on steroids – compressive structural bioinformatics

PDB needing to work with larger structures and more data. 120,000 structures in June 2016. Need to have ways to compress and manage data for storage. For analysis, hold in memory on the cluster and run analyses using Apache Spark. Provide custom compression in MacroMolecular Transmission Format, using messagepack for compressed JSON-like binary.

Robin Andeer – Puzzle: VCF/GEMINI interface for genetic disease analysis

Puzzle designed to handle human genome analysis of VCF files. VCFs are complex so need standardization for improved analysis, including visualization. Will suck up a directory of files and prepare for visualization. Can handle VCF, BCF and Gemini databases. Viewers for structural variants, standard variants.

Keiichiro Ono – Modernization of the Cytoscape ecosystem

Cytoscape is a popular platform for network analysis and visualization. It has a single small core, layered with core apps and community third party apps with ~300 applications. It’s an application publishing platform for network biology. Many tools written in non-Java – how can you integrate well with Cytoscape? Support multiple plugins now at CyWiki.

Abigail Cabunoc Mayes – Collaborative Software Development: Lessons from Open Source

Abby is the lead developer for open source engagement at Mozilla Science Lab. History: netscape released as free software – want to bring this ethos to open source. Need to be public and participatory: structuring events so outsiders can participate and become insiders. Inspiration from Disney: do a great job of showing you the right way to go. Open Source checklist: public repo, open license, readme, roadmap, code of conduct, contributing and mentorship. Need to be better at this in bcbio. Mozilla Fellowships – bring open ethos to your community.


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