Scientific Python 2013, Day 2: Bioinformatics frameworks, open science and reproducibility

I’m at the 2013 Scientific Python conference in beautiful Austin, Texas. I’m helping organize this year’s Bioinformatics Symposium and learning about Python scaling and reproducibility from the Scientific Python community. These are my notes from the second day. See also my notes from the first day.

Ian Rees – Bioinformatics symposium: electron microscopy platform

Ian talked about software to handle data challenges associated with imaging. They principally focus on imaging of macromolecules using Cryo-EM. There is then a ton of processing before this can get into PDB as structures. 300+ active projects. Focus on archival, automation of record keeping, understanding how protocols change over time and sharing results with collaborators.

EMEN2 is their solution: a object-oriented lab notebook. It uses a protocol ontology to allow flexible queries of approaches. Take a general approach to connect records. Impressive display of a long 10 year project with 15,500 records. Records look like json documents of key-value pairs. Built on top of BerkeleyDB, with a twisted web server. Provides integrated plotting and viewing of results, in addition to table-based viewing of projects and samples. Hooks in with the microscopy software so data uploads automatically. It provides a public API with JSON to query the data with a constraint based query language. Also has python hooks to create extensions with controllers and mako templates.

The connected image processing toolkit is EMAN2.

Larsson Omberg – Bioinformatics symposium: Synapse platform

Larsson discussed the approaches and tools that SAGE bionetworks use to help improve reproducibility of science. The Synapse tool tries to handle reproducibility on a distributed scale with multiple collaborating scientists, as opposed to other projects which focus on single researchers. Example of usage for the cancer genome atlas: 10,000 patients, 24 cancer types, and multiple inputs: variations, RNA-seq. Biggest challenge is coordination of multiple data sources and inputs. Data automatically pushed into Synapse, then do data freezes to allow analysis. Analysis results get pushed back into Synapse as well.

Synapse is a web framework that allows multiple usages of tools in multiple places, and register results back with Synapse to coordinate results. Python API allos you to query with SQL syntax and retrieve specific datasets which have key/value style metadata annotations in addition to the raw data. Impressive demo of uploaded results with lots of metadata: nice way to understand custom analysis and review results.

Synapse focuses on avoiding the self-assessment trap by moving this assessment into a centralized location. Also run challenges that help formalize this: Dream8 Challenges.

Joshua Warner – scikit-fuzzy

Joshua talked about his implementation of a SciPy toolkit for fuzzy logic: scikit-fuzzy. Has fuzzy c-means for smaller uses and needs full Cythonization. Has 100% test coverage. Provides foundational tools for fuzzy logic but focusing on community building to provide additional tools. Good questions about the most useful places for fuzzy logic usage: it’s a good prototyping step which includes some insight into the logic intuition for understanding approaches. It’s not especially useful for categorical variables.

Jack Minardi – Raspberry Pi sensor control

Jack talked about interacting with Raspberry Pi using pyzmq: controlled LEDs and motors. Raspberry Pi has general purpose input output pins which allow you to interact with other external devices. Used the Occidentalis Wheezy based operating system which provides a lot of pre installed tools over the base installations that Raspberry Pi recommends. Jack live demos blinking an LED, which one ups live software demos for sure. Another cool demo uses pyzmq to stream the xyz location of a device to a real time plotting tool.

There are an incredible number of open source tools for Raspberry Pi on GitHub that help manage interacting with the different hardware. There is a cool community around working with it.

Raspberry Pi and other hackable hardware tools also provide a wonderful teaching environment for programming. It is so much more satisfying to make something happen in real life, and teaches all the important skills of installing, learning and debugging that you need in any kind of hacking. On a larger scale in genomics, efforts like the polonator from George Church’s lab offer an opportunity to learn all the hardware behind sequencing

Jeff Spies – The Open Science Framework

Jeff discussed work at the Center for Open Science to build infrastructure and community around opening up science to reduce the gap between scientific goals (open) and science practical needs (papers, funding). Problem is that published science is not synonymous with accurate science. Worry about unconscious biases like Motivated Reasoning. Approach of OSF is to provide tools that work within scientific workflows to enable and incentivize openness. The Open Science Framework provides a simplified front end to Git, handling archiving and versioning of study data. Provides unique URLs to tag specific versions for publication. Goals are to make components API driven to allow other interfaces like IPython notebooks.

Burcin Eröcal – scientific software distribution

Burcin discussed approaches to replicate, build on and improve scientific work. Shows an example of Sage, which has multiple requirements and installs well: installation matters, a lot. His approach is lmonade, which provides customizable distribution of scientific software. Burcin does not think virtual machines solve this problem because they are not programmable to add updates. I wonder if lightweight solutions like docker help mitigate some of these concerns. In general, I haven’t heard any usage of virtual machines at SciPy which makes me sad because I think this is an important path for moving forward with complex installations. He also compares to the nix package manager. The main issue with this is that it requires explicit definition of dependencies so not as flexible as scientific software needs.

John Kitchin – emacs org-mode for reproducible research

John discussed using emacs org-mode to create reproducible documents with embedded python code. John’s GitHub has tons of useful example of using this for blogging and book writing. Impressive demos, I need to dig into his org files for tips and tricks.

Lightning talks

Travis talked about solutions to packaging problems in Python: conda and Look like useful alternatives to pip that might help with lots of installation problems we see with multiple dependencies. The Conda recipes GitHub repo has lots of existing tools.

Matt Davis gave a great advertisement for Software Carpentry. It’s a wonderful resource for teaching scientists to program. They also need teachers and help from the community, so volunteer please.

BLZ is a high IO distributed format inside of Blaze. The BLZ format document has additional documentation. This all gives you a distributed NumPy operating on massive arrays.

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