Tag Archives: Cytoscape plugin

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Friday SNPpets

This week’s SNPpets include stories about how DNA gets into the databases, network visualizations, historical genome browsers, CVS doing personalized medicine, fungal genome resource issues, mouse, dog, plant and human data stories, free data, and more.


Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


https://twitter.com/timknut/status/628194770649804800

https://twitter.com/howplantswork/status/628198284658475008

What’s the answer? Cytoscape plug-ins

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

Question of the week:

Cytoscape Plug-in for retrieving Protein-Protein Interactions

I wish to find out all interactions WITHIN a set of around 200 HUMAN proteins. The identifiers I can use are gene_name, Uniprot_accession and Uniprot_Ids. So far I tried two plugins viz. MIMI and APID2NET.

MIMI doesn’t seem to accept 200 proteins in one go, so I’ve to merge the networks. APID2NET shows too many nodes without any interactions. The STRING DB shows quite a many interactions for which MIMI/APID2NET don’t report anything.

I tried the STRING plugin too, but it looks like it can accept one ID at a time. Am I missing something here?

Can somebody recommend some good and hassle less plugins/tricks to import PPIs. I’ve to do subsequently a BINGO analysis.

Thanks in advance

–WoA

Although most people in this arena will be familiar with Cytoscape, it can be challenging to know which specific plug-ins might be best for a given purpose. One of the cool things about a forum like BioStar is that there is a range of folks who have wide experience with the tools from so many different projects that often someone has a bit of guidance on things that did (or didn’t) work.

In this case someone offered a suggestion that seemed to fit the bill precisely! Check out the answers, and note the selected () answer to see which it is. It’s a tool I noticed in the past partly because it was the first bioinformatics tool that I had seen that came from Cuba and I thought that was cool–BisoGenet.

But if you have other suggestions you can also offer them at BioStar.

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • A WordCloud Plugin for Cytoscape is now available from the Gary Bader lab. You can read a description of it and download it on this page. [Jennifer]
  • Undergraduate Guide to R by Trevor Martin; hat tip to Storey Lab for that. [Mary]
  • Cool resource, hat tip to James: “Just discovered MorphBank, a database of creative commons licensed images of biological specimens: http://www.morphbank.net” [Mary]
  • Clinical trial for “Finicky Eating in Adults” (F.A.D.) – read a description and fill out the survey, if you are 18+ yrs old, a “picky eater”, and meet other criteria. [Jennifer]
  • GenAge: The Ageing Gene Database. Found this via tweet by attilacsordas, whose code was apparently involved in implementation of this. (I’ll bet that gets even hotter as a topic when boomers get their genomes sequenced…) [Mary]