Tag Archives: Biocatalogue

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…

  • This is not a bad idea. Boston Sci-Geek Tours. I used to work for the Park Service. Hmmm… RT @YishaiKnobel: Fascinating tour and lecture on genomics at Broad Institute today.  Broad should be turned into a Boston tourist attraction. [Mary]
  • RT @BioCatalogue: The BioCatalogue iPhone/iPad app by @manniet3 is now out! http://bit.ly/p2tUQF Please do let us know what you think. [Mary]
  • Includes KEGG, iPATH 2.o, PathwayProjector, metaSHARK, MEGAN 4,  HUMAnN: RT @phylogenomics: A Survey of Metabolic Reconstruction Tools for Metagenomic Datasets » The Bioinformatics Knowledgeblog http://shar.es/HK0U5 [Mary]
  • A Special Symposium Celebrating the 40th Anniversary of the Protein Data Bank, October 28 – 30, 2011, Cold Spring Harbor, NY – Poster Abstract deadline: August 15 [Jennifer]
  • Oh yes, plz: RT @nutrigenomics: like RT @grapealope: Bioinformatics is not just about building tools. We know our tools; we should use them first. @atulbutte #singularityu [Mary]
  • Giggle. I’ve done this with several species, not just plants… : @pcronald: Botanist holds up the entire salad bar. http://onion.com/pojv2t [Mary]
  • RT @wahwahnyc: On PubMed Central: The PathOlogist: an automated tool for pathway-centric analysis. BMC Bioinformatics. http://1.usa.gov/oDyBpc [Mary]
  • Looking for some geeky fun? The Twenty-First 1st Annual Ig Nobel Prize ceremony will occur Thursday, September 29, 2011 and tickets are on sale now. Note: “The Ig Nobel Prizes honor achievements that first make people laugh, and then make them think.” [Jennifer]
  • RT @genetics_blog: . @PLoS and @mendeley_com Call for Apps: http://bit.ly/oc2NGL and http://bit.ly/nHYqNa [Mary]
  • Just saw this in Nature News about Google and Microsoft: Computing giants launch free science metrics [Jennifer]
  • FameLab, a science and engineering communication competition – I haven’t seen an uninteresting one yet… [Jennifer]

Tip of the week: The Taverna Project for workflows

We’re on the road this week doing workshops, so I needed to have this tip prepared well ahead of time. To make it easy on myself, I’m going to simply point you to a recent informative webinar on Taverna, that was hosted by Bitesize Bio (and check out their other upcoming webinars).

The image I used as the screen shot made me laugh. It was a graphical illustration of what you might need to do to analyze a piece of sequence data that you might obtain. You have to leap around to all kinds of sites and tools and they all stand nearly independent of each other, and if you wanted to do it with another sequence later you’d have to face the same series of events. Workflow tools are now being developed to streamline, automate, and simplify this process.

Taverna is an application that supports bioinformatics workflows (and other types of workflows as well, actually).  It combines with the MyExperiment social networking aspects, and the BioCatalogue collection of web services. You can create complex and effective workflows, share them with others, and store them for re-use.

If you are considering using workflows to at least partially automate some of the processes you need to accomplish, you should know about Taverna. And this webinar is a nice introduction to the basics and philosophy around it.

It was just over 30 minutes if I remember correctly. And you can hear my question at the end–I asked if the version numbers of software tools or data sets is stored with the analysis. The short answer: no, it’s up to you to do that. [This is something that concerns me a lot about workflow tools and I try to press for this all the time.]

Currently I use Galaxy for the workflows I need. But recently it was announced that there’s a way to use eGalaxy with Taverna to generate workflows that can run in Galaxy–but I haven’t explored this at all yet.

Quick links:

Taverna Webinar at BiteSizeBio: http://bitesizebio.com/webinars/the-taverna-project/

Taverna application: http://www.taverna.org.uk

Tip of the Week: BioCatalogue for finding web services

A couple of years back at a conference I was introduced to BioCatalogue.  It seemed to me to be a really useful idea: locate bioinformatics tools and databases that are web-accessible, and that also have a mechanism to use the web service features to access the tool/server using strategies that don’t require the main web interface of the site.  There are some introductions  to the concept of web services out there–some of them are more for introduction, but most are aimed at programmers.  Essentially it is kind of a back door into the tool, and lets you pull the information you need out in ways that you want–not constrained by the main user interface.

BioCatalogue is a curated collection of these web services.  The creators  of BioCatalogue provide the framework and perform some of the  collection and annotation–but they also enable the user community to bring in web services and annotate them as well.  This means that you can use BioCatalogue to find and learn more about the services, and you can feed back into the system as well if you join the community.  If you are a software provider you can register your service there–so more people can locate you and learn about your project.  Another really nice aspect of BioCatalogue is that they monitor the services.  As we know at OpenHelix–plenty of times a tool you have accessed in the past is suddenly unavailable.  Sometimes they are intermittent server problems, but sometimes they are longer-term issues.  BioCatalogue is regularly checking  the status of the tools so you can have confidence that the tool has been up and seems stable.

The Web Server issue (see the 2009 issue here) of Nucleic Acids Research provides a wealth of  information about useful servers with bioinformatics tools.  And there’s a paper for the 2010 Server  issue about BioCatalogue that will offer more details on the background (linked below).  In this week’s movie I can only briefly introduce the site and the features available.  Check out the paper from the BioCatalogue team, and explore the documentation wiki to learn more about the features and functions that are  provided.

Now, these web services are not for everyone.  For many people the main user interface will still be the best mechanism to access a tool. But if you need more advanced or customized queries, or if you want to create inflows into your own tools, or if you want to use some of the cool work flow software that’s  out there now (such as Galaxy or Taverna)–web services may be right for you.

Check out BioCatalogue  (and remember the -ue spelling!) http://www.biocatalogue.org/

Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., Wolstencroft, K., Aleksejevs, S., Stevens, R., Pettifer, S., Lopez, R., & Goble, C. (2010). BioCatalogue: a universal catalogue of web services for the life sciences Nucleic Acids Research DOI: 10.1093/nar/gkq394