Tag Archives: Cytoscape

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…

Priorities when the workplace is on fire:

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…

  • Wait, where is the $100 genome exactly? I must have missed a tweet somewhere RT @deanhendrix: If we can sequence a human genome for $100, why can’t we openly publish for $100? http://t.co/JUIg5HnZ via @thePeerJ #openaccess #cmonnow  [Mary]
  • RT @genetics_blog: NAR: Most conserved non-coding sequences are regulatory factor binding sites http://t.co/kcFwPeZ7 #bioinformatics [Mary]
  • RT @bffo: Very cool, new cystoscope App store http://t.co/u8gbLiAk #Bioinformatics [Mary]
  • Heh–fair point: RT @phylogenomics: At end @mjpallen says “Radio has survived alongside TV” in reference to how traditional microbiology will survive alongside genomics #SAMG12 [Mary]
  • RT @mem_somerville: Was looking up old story, realized that Nurse, Venter, Collins all have motorcycles. Want to see them race. (must be a gene…) [Mary]
  • @OpenHelix: RT @genome_gov: #microbiome Mapping of human microbiome produces insights, surprises. http://t.co/TYiXCvgX [Mary]
  • And then… RT @matthewherper: Was The Human Microbiome Project A Waste Of Money? – Forbes http://t.co/Crb9eFzo via @sharethis [Mary]
  • And then…snorf:
  • Oooh boy: RT @drbachinsky: Hay Festival 2012: Dull middle-aged scientists should not get grants, says DNA pioneer James Watson via @Telegraph http://t.co/1iGAfFof [Mary]
  • I want to photosynthesize. RT @Argent23: The next twist in the Elysia story. Seems like >50 algal chloroplast genes were transferred into the slug genome! http://t.co/fDJ4iJYa [Mary]

Special Bonus item: if science had tabloids—you have to go see Francis Collins and Fred Sanger “Hot Pics!” http://fakescience.tumblr.com/omgscience

Video Tip of the Week: GenomeSpace, an integrator of integrators


Recently, the Broad Institute announced a new tool: GenomeSpace. When I first looked at it, admittedly a very cursory look, I wasn’t sure how it would be much different than an integrator of tools like Galaxy or GenePattern. Obviously that cursory look was wrong at first glance since both Galaxy and GenePattern are in their list of tools that are supported. So what is GenomeSpace? Well, you can read the answer here at their “What is GenomeSpace” page :). Basically, GenomeSpace has several functions. As described here, “GenomeSpace supports several bioinformatics tools, all integrated to allow easy accessibility, easy conversion, and frictionless sharing.” It is a space (in that every expanding Amazon cloud) that allows you to store your data files and, importantly, GenomeSpace allows you to seamlessly move those files between the tools to complete complex, or simple, analyses. It achieves this by automatically converting file formats and by allowing the user to attach their accounts at the tools to their account at GenomeSpace, thus alleviating the need to log in several times when using more than one tool.

To get a good idea of what GenomeSpace might be able to do for a researcher, check out the recipes on the site. As Anton  states:

GenomeSpace is an integration of integrators,” Nekrutenko said. “The benefit to the user is that this brings together distinctive collections of functionalities offered by individual tools.”

The site is new, and only in beta. They only recently opened up registration from their invite-only stage. As such, there are some bugs and some features that aren’t quite at full capacity. For example, the Galaxy and UCSC Table Browser integration is with the test versions of those tools during beta. Thus, for example, your account at Galaxy will not be recognized when trying to link that account with GenomeSpace. I had to create a new one on the test site. And, if you go to the public version of the Table Browser, it will look different (no link to GenomeSpace as there is on the test site). Currently there are seven tools, more to come.

All that aside, it’s definitely a tool to get acquainted with. And with that in mind, take a quick introductory spin with me in this week’s video tip to get an idea of what you might be able to do.

Quick Links:

GenomeSpace
UCSC Table Browser (OH tutorial)
Galaxy (OH Tutorial)
Cytoscape (OH Tutorial)
Genomica
GenePattern
IGV
InSilicoDB

Broad Institute
NHGRI 

 

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…

Guest Post: iRefWeb — Andrei Turinsky

This next post in our continuing semi-regular Guest Post series is from Andrei Turinsky, one of the developers of iRefWeb. If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey something to users on our guest post feature, please feel free to contact us at wlathe AT openhelix DOT com or the contact form (write ‘guest post’ as subject heading). We welcome introductions to your resource, information on updates, highlights of little known gems or opinion pieces on the state of genomic research and databases.

What is iRefWeb?

Protein-protein interactions (PPI) have become an important tool in biomedical research. Yet the PPI data for a specific organism tend to be distributed over a number of different databases. Comparison and integration of PPI information across databases remains a challenging task.

iRefWeb (Turner et al. (2010) Database, Vol. 2010, Article ID baq023.) is a web interface to a broad integrated landscape of protein-protein interactions (PPIs). For a given gene or protein, you can access all PPI records and protein complexes, consolidated non-redundantly from ten major public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb also presents various supporting evidence, helping you to gauge the reliability of an interaction. Versatile search filters allows you to retrieve the PPIs with a given level of support. Other features facilitate the analysis of possible inconsistencies across PPI data and the examination of PPI statistics. Data consolidation procedure effectively combines redundant records using the iRefIndex process (Razick et al (2008) BMC Bioinformatics 9, 405.).

Figure 1: The iRefIndex process aggregated over 916,059 original PPI records from source databases, 75% of which were redundant. The consolidation merged the redundant PPIs, reducing their number four-fold (orange). Only 232,612 PPIs were non-redundant (blue)

Continue reading

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]

I ♥ Venns

Ok, I know they aren’t the most sexy graphics in biology–yes, you 3D protein structure geeks have that down. They are a pretty straight-forward representation of the numbers of items in a group and the overlap. But I have always found them really quickly helpful as I’m trying to assess results of lists of things I may have been working on.

So conveniently enough I just got a notice of a new Venn tool today–and it’s a Cytoscape plug-in. That’s a sample of one of the components of it on the right.  And I just happen to be working on the update for our Cytoscape tutorial this week (subscription), so I’ll be able to add it to our tutorial.  Anyway, here’s the notice as it came across the Cystoscape-announce mailing list:

Cytoscape plugin for venn diagrams, version 0.2 has been released.

The plugin provides a diagram view and a details view for comparing two to four Cytoscape groups at a time.

Project web site http://www.dishevelled.org/venn-cytoscape-plugin

Downloads http://sourceforge.net/projects/dishevelled/files/venn-cytoscape-plugin

Screencast http://www.youtube.com/watch?v=UtoW0nVwOV4

This plugin is for Cytoscape version 2.7.0 only, an incompatible change was made in Cytoscape version 2.8.0-beta that hasn’t been resolved or worked around yet.

michael

And they even offer a screencast on it. Check out the interactive capacity of that–a segment of your Venn gets highlighted back on your network/pathway window. How nifty. Made my morning!

Are there other Venn tools out there that people use and like?

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 Cuban bioinformatics group announces updates to their Cytoscape plug-in. “A new update of SysBiomics database is ready. SysBiomics contains the data feeding BisoGenet network building process; it was updated with most recently versions of protein-protein interactions sources (DIP, BIOGRID, HPRD, MINT and INTACT), GO and KEGG databases as well as the latest information on genes an proteins form Entrez Gene and Uniprot .” Bioinformatics Group http://bio.cigb.edu.cu/ Cool–I think that’s the first tool I know about from Cuba.  [Mary]
  • “In October’s “Nature Genetics”, and just in time for pie-making: http://www.ncbi.nlm.nih.gov/pubmed/20802477 …but where’s the gene that keeps the doctor away?” [Trey, via a colleague's email :) ]
  • Cool new site on the History of Vaccines. Hat tip to Tara at Aetiology. [Mary]
  • RT @kshameer: RT: @suganthibala: 200 exomes resequenced, found many rare nonsyn SNPs http://bit.ly/bjm2Q6 http://bit.ly/ctQJ59 #genomics #bioinformatics [Mary]

Friday SNPets

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…