Notes: Bioinformatics Open Source Conference 2014 day 2: Philip Bourne, Software Interoperability, Open Science

I’m at the 2014 Bioinformatics Open Source Conference (BOSC) in Boston. It’s a great two day conference devoted to open source, science and community. These are my notes from the day 2 morning session. Next Day Video recorded all the talks and they’re available on the Open Bio video site.

Other notes:

Biomedical Research as an Open Digital Enterprise

Philip Bourne

Philip starts off apologizing for not writing a line of code in the last 14 years. He talks about current funding issue in science: lack of growth in NIH funding but exponential increase in biological data. Hard to quantify right now: how much do we spend on data and software? Futher, how much should we be spending to achieve the maximum benefit? Biggest current issue is reproducibility; critical to improve public perception of biological research as well as fundamentally important to good science.

From a funders perspective, it’s a time to squeeze every penny to maximize the amount of research that can be done with money. Two approaches: top down and bottom up. Top down: regulations on data, data sharing policies, digital enablement and move towards reproducibility. Emphasizes the importance of discussions between communities for working with large data. Bottom up approaches: collaboration, open source and standards.

Mentions the current issue that software developers are in great demand, and rewards outside of academia are greater than inside. Need new business models and software best practices. Current challenge: elements of the research life cycle are not connected. Presents nice graph of areas where he feels like we’re doing well and struggling.

Presents public/private partnership called The Commons. Idea is to have agile pilots testing out ideas and new funding strategies. One example, porting dbGAP to the cloud. The commons is a conceptual framework, analagous to the internet. Meant as a collaboration using researching objects with unique identifiers and provenance. Commons meant to handle long tail of data that does not fit anywhere, high throughput data from big facilities and clinical data rules. Brilliant, smart and on-point ideas: excited about what NIH/NSF is doing.

What does the Commons enable? Dropbox like storage, quality metrics and metadata, bringing compute next to data, and giving places to collaborate and discover. The most critical element is establishing a business model: current thinking is to provide a broker service. Idea to is have a series of pilots to evaluate, and hoping to make decisions by 2015.

Great discussion questions. Ann Loraine: 20% time on grants for more exploratory research. Titus Brown: how can we speed up review/grant process to work with agile processes? Thomas Down: can we improve incentives/fun for making data available? Currently not as fun as actually doing science. Really awesome to see so much discussion during Philip’s talk.

Great example of current software folks to talk to: MyExperiment, Galaxy. Also would suggest iPlant, SAGE Synapse, Figshare. Lots of new Big Data to knowledge (BD2K) grants coming.

Overall talk idea is to foster an ecosystem of biomedical research as a digital enterprise.

Software Interoperability

Pathview: an R/Bioconductor Package for Pathway-based Data Integration and Visualization

Weijun Luo

Pathview provides pathway visualization using KEGG-based pathway. Bioconductor R package. High level API calls to get very nice visualizations of multiple sample experiments layered on top of named pathways. Nice automated segmentation and labeling of attributes. Supports over 3000 species: everything in KEGG with sequenced genomes. Takes care of ID mess by supporting everything. Nice workflow for running RNA-seq processing, then feeding into Pathview and GAGE for visualization.

Use of Semantically Annotated Resources in the Mobyle2 Web Framework

Hervé Ménager

Mobyle is a web-based bioinformatics workbench. Currently working on Mobyle2 re-write which includes groupware functionality, secure data sharing, REST API and ontology bsaed annotations. Re-write deals with issues with current classification and typing systems, specifically designed to provide improved sharing. Ontology describes relationships using EDAM ontology. With these, can now annotate formats of inputs/outputs to enable automated conversions and improved chaining of tools. Can also do cool stuff like automated splitting.

Towards Ubiquitous OWL Computing: Simplifying Programmatic Authoring of and Querying with OWL Axioms

Hilmar Lapp

Hilmar describes work done by Jim Balhoff at NESCent on using RDF and OWL to improve computational data mining. Done as part of PhenoScape project with the goal of understanding causes of diversification. Very difficult to author ontology axioms at scale: translating complex assertions into rules make my head hurt. Scowl tool provides a declarative approach to defining these. This also helps make ontologies easier to declare and version control. Similar work is Tawny OWL from Phil Lord. Second tool is to handle Ontology driven queries in SPARQL: owlet. Vision is to make programming with ontologies easy: small tools to fill gaps and holes.

Integrating Taverna Player into Scratchpads

Robert Haines

Describes works integrating Scratchpads and Taverna. Scratchpads are websites that hold data for you and your community. Scratchpads is a Drupal backend with lots of models: 500 sites using this system hosting on two application servers. Taverna provides the workflow system and uses Taverna Player which is a Rudy on Rails plugin that talks to Taverna’s REST interface. Wow, a lot of Taverna calling Taverna calling Taverna: very modular setup. The integration happened to joining two biodiversity communities and make it easier to disseminate data via Scratchpads. With Taverna allows running on this generalized disseminated data. Interesting work to have multiple ways to do this: both tight and lightweight integration.

Small Tools for Bioinformatics

Pjotr Prins

Pjotr talks about approaches to improving how we can better integrate tools, manage workflows. Bioinformatics is often about not invented here and monolithic solutions. Does this happen because of technology and deployment. Wrote up a Bioinformatics Manifesto to build small tools, which should each do the smallest possible task well. Idea is to make each part anti-fragile so the whole system can be more robust. 3 examples of tools that do this: Pfff is a replacement for md5 comparisons that samples files so scales to large inputs. sambamba is a great tool with samtools like functionality and parallelization. bio-vcf is a fast VCF parser and filtering tool.

Open Science and Reproducible Research

SEEK for Science: A Data Management Platform which Supports Open and Reproducible Science

Carole Goble

Carole talks about SEEK work enabling systems biology, linking models and experimental work. Idea is to preserve results, organize data, exchange and share data. Difficulty in dealing with home-brewed solutions from each lab. Tricky to deal with both small and large data, lots of different inputs to mix together. Catalogue data as the critical component using ISA metadata. They integrate a crazy incredible number of standards and other tools in general; beautiful reuse. Use Just Enough Results Model (JERM) to describe relationships between everything done in experiments. Research Object provides nice way to provide tagging and provenance of research work. Funded to extend this as open system for european systems biology data.

Arvados: Achieving Computational Reproducibility and Data Provenance in Large-Scale Genomic Analyses

Brett Smith

Arvados is a open source platform for managing and computing on biological data. Parts of Arvados: Keep provides immutable content addressable storage, providing git-like behavior for data. Objects tracked and managed through the Arvados API server. Jobs submitted as big ol’ JSON format. Uses Docker to manage images. Everything gets GUID identifiers for data, code and docker images so get provenance for everything run.

Enhancing the Galaxy Experience through Community Involvement

Daniel Blankenberg

Dan describing work to involve the Galaxy community in development and analysis. He starts by describing all off the awesome stuff that Galaxy does with shout out to Galaxy on AWS using CloudMan. Interesting stats on running jobs on Galaxy main – leveling off due to complete usage of resources: need to diversify big jobs on Cloud or local installations. Awesome plots of community code contributions, 51 unique users in the past year. They’ve moved to BioStar interface for answering questions.

Open as a Strategy for Durability, Reproducibility and Scalability

Jonathan Rees

Jonathan motivates with example of chicken evolution; my son would love this. The problem is that the tree of life is hard to find, hence the Open Tree of Life. Nice resource and love the continued chicken examples; ready for a viewing of Chicken Chicken Chicken. Has nice browser and API views to the tree. Trick part is getting the trees, which references back to Ross’ talk yesterday. Big emphasis on actually open data (CC0) and publications (CC-BY). All data going into GitHub as JSON.

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