Video Tip of the Week: InSilico DB

Before the holidays I had seen this paper on InSilico DB come out, but I didn’t have a chance to really explore the site very much. I was reminded again of it when I saw this tweet with a handy summary:

RT @schelhorn: InSilico #database for querying public #genomics #data sets (think Google for GEO) http://t.co/5Buzy7jv

But now that I’ve had a chance to look around some more, it looks to me like InSilico DB offers some nice integration of data sets, with useful tools and output strategies that are worth exploring.

With a large collection of public data sets that have been integrated from a variety of sources, InSilico DB offers a quick way to browse, search, and filter for genomics data that’s relevant for your work. As of the time of the publication, the collection consisted of nearly 7000 samples, from sources such as:

InSilico DB contains a large number of microarray and NGS datasets originating from public repositories, NCBI Gene Expression Omnibus (GEO) [25], Short Read Archive (SRA) [26], The Cancer Genome Atlas project (TCGA) [27] and the Broad Institute [28].

It also enables you to curate and edit features that will help you to organize and find what you want from these public data sets. But it also permits you to add your own data to the collection–either privately or publicly–and share them with your team.

But another really useful aspect involves the ability to take the data you have found and edited and export that data to other tools for further analyses.

InSilico DB facilitates analysis by enabling a ‘one-click export’ of genomic datasets with curated clinical annotations to specific analysis platforms. Currently supported formats are R/Bioconductor [40], GenePattern [41] and IGV [42].

So you can take your research further in a variety of ways.

I’m highlighting one of the videos that they created to give you an idea of how you can work with InSilico DB, but be sure to check out the other guidance they have in their tutorials section, and keep an eye on their blog for updates and other features too.

Quick link:

InSilico DB main site: https://insilicodb.org/

Reference:

Coletta, A., Molter, C., Duqué, R., Steenhoff, D., Taminau, J., de Schaetzen, V., Meganck, S., Lazar, C., Venet, D., Detours, V., Nowé, A., Bersini, H., & Weiss Solís, D. (2012). InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor Genome Biology, 13 (11) DOI: 10.1186/gb-2012-13-11-r104