Thanks for Open Source Research

Keeping with the holiday spirit, this blog will offer thanks to some great open source research projects.  Having returned from Neuroscience2017 recently, two organizations’ work really moved above the pack.  Yea, Neuroscience2017 was HUGE, but we were there to support a client’s presentation of our collaborative bioinformatic contract work and he did great!  Anyhow, the neuroscience data powerhouse is the Allen Institute’s Allen Brain Atlas and it’s connectivity map and well, while it claims to be an open source project, it has commercial limitations.  This then, is not open.  Scouring the exhibits and posters at Neuroscience2017, A2IDEA found two sources that may make it much easier to search, obtain and use neuro related databases.  These are Neuroscience Information Framework (NIF) and Sage Bionetworks.  

The NIF is pretty nifty.  This catalogue, self described, has the largest listing of NIH-funded, neuroscience-relevant resources.  Basically, it’s a gateway that ports a host of different web resources, LIKE … over 800 Million results from 270 database.  It includes antibodies, cell models, clinical trials, imaging, grant funding information, and the typical stuff we look for; gene transcription data, protein-protein interactions and software tools.  While this resource is truly open, some of the databases and resources it brings in may not be, so buyer beware.  However, this is a great resource and jumping off point to find information regarding neuroscience.  It even has it’s own community bought-in vocabulary and ontology; NeuroLex.  This allows user through a single interface, search across multiple informational sources to really integrate knowledge.  

Secondly, while we already knew about Sage Bionetworks work in Cancer Research, they are also doing some really cool stuff disease and/or system agnostic.   While at first it can take some time to get through all the intro stuff, get an account, it’s worth it.  The Synapse API resources by themselves can buy back that time, more on that below.  

Synapse from Sage Bionetworks is a research platform in the truest meaning.  In it’s simplest form, one can download data.  They link to ally types of data, some that can be very hard to find… like what are the concomitant medications for 115 kids with Type 1 diabetes in a clinical trial monitoring immune supression?… it’s there.  But say, you’re not interested in all the data they have and you’re more looking for a platform to enhance collaborative research, as we at A2IDEA are often asked to perform.   Ya know, something a little more sophisticated than just BitBucket and / or GitHub.  The answer is Synapse, one can make a project, upload / transfer data into that project and work in a collaborative environment to really carry out large scale distributed research.  There’s some great API’s in python, R and even command line along with some comprehensive documentation.  And your project work can be kept private while working along, but they have great tools to release and share the data when you want.  We all know that most analytical research (even in silico) is experimental and ad hoc in nature, with hardened analysis methods only emerging over time. Tracking who has run what version of code on what version of the data immediately helps projects run more smoothly, and ultimately enables reproducible workflows that allow others to build off of prior work.  This is where Synapse from the folks at Sage Bionetworks really shines.  We at A2IDEA are thankful!