Tools

Today, I’m going to continue down the path of free resources for continue learning.  There are numerous, free online resources for the analysis of data.  Like, a TON!  Each and every week my news feeder is filled with at least 2-3 new tools that can do this, or that, and hopefully improve upon the current methods and tools.    

However, there are two resources for ‘omic’ tools that are worth mentioning.  The first is Bioconductor.  This is an amazing resource for any bioinformatician or statistician.  It’s solely used for programing in R, is open source, and has a host of packages for a bioinformatician to use.  The great part about this site is all the training materials.  For the most part, the packages posted on Bioconductor are vetted, have great user manuals, and have an active community for users to ping in case of trouble.  The support is just phenomenal.  

Secondly, Omic Tools is a curated listing of many ‘omic’ related tools.  And not just ‘omic’ analysis tools, but it also includes LIMS system software, Venn diagrams, data repositories, NMR readers, protein visualization tools.  While it is curated, there are no official user manuals, or active community to aid in troubleshooting a particular application listed on the website.   It’s basically a listing, description and map of available tools.  There’s no guarantee that the tools listed are still supported by the authors, or whether anyone will help in case of issues.  

Lastly, and worth mentioning, are the open-access publications such as BioMed Central and PLOS that includes Genome Biology, BMC Bioinformatics, PLOSone, and many others that offer amazing resources for anyone interested in analyzing diverse ‘omics’ data.  These publishers not only make all their publications open-access but strongly encourage authors to make all their tools and data open-access.   Like I said, there’s no shortage of available tools.  It’s the use of the tools that can be problematic.  

Everyone that works for A2IDEA closely monitors new tools and applications.  After all, it’s our domain, our preferred technical reading, and our passion professionally.   While we constantly monitor the above resources, and others not listed, for new and exciting tools, we don’t always adopt every application that comes available.  We test and analyze, and then test some more.  Only after it passes our rigor and fills our customers’ needs, may we decide to adopt.  Or, we may decide to improve upon the idea recreating from first principle.  

So, if you’re the type that likes to do your own analysis, please use the above fo find an  application that’ll fit your needs.  If you’d rather have us analyze your data, and then teach you our methods, we’d be happy to help.  In the end, these are tools and while I personally can turn a wrench, I know not to try to fix any serious home plumbing issue.  Tools are only as good as the person on the other end using them.