The OpenHelix Blog

About 6-7 months ago, Mary mentioned that R-Genetics analysis was coming to Galaxy. Well, it has now and is available at the public Galaxy site. The old Rgenetics site links to the new one and the information about using Galaxy as a wrap around interface for the Rgenetics project tools. Today’s tip just points you to the tool and gives you a quick overview of what is there. You’ll need to do some exploring to learn to use it! Of course, we have our publicly available Galaxy tutorial to get you started.

(oh, and I point you to this tutorial on analyzing Desmond Tutu’s SNPs using Galaxy that I thought was interesting)

Welcome to our Friday feature link dump: 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…

• Accessing SEED genome databases via web services, hat tip to Jonathan Eisen. [Mary]
• Galaxy team wants to discuss location for the 2011 Developer’s Conference in Europe. @bffo suggests Vienna during ISMB. [Mary]
• Interesting comments w/ good article links on this CBC News article “MDs warn of online stem cell therapies” [Jennifer]
• Website mentioned in above article is found here, I believe. [Jennifer]
• Microsoft Biology Foundation v1.0 Ships – http://ow.ly/2dZz2 Via Paul Blaser. [Mary]
• Much buzz this week on the great newbie guide to GWAS interpretation at Genome Unzipped. [Mary]
• Pretty interesting results featured in The Scientist this week: Better housing fights cancer in mice, original research article here, if you subscribe to Cell. [Jennifer]

Sorry for the sparseness of late. We were all  over the place doing UCSC Genome Browser (we do intro + advanced), ENCODE, and Galaxy workshops.  At NIH we also did IMG and VISTA (Man, that security at NIH is fierce….).  Trey is still on the road, in fact, doing the training in Morocco.

Ok, you couldn’t be there…but all of those trainings are available on our web site right now, except for ENCODE. The same material we do in the online materials is what we do in workshops. The only one of those that requires subscription is IMG. And you won’t find ENCODE as a stand-alone tutorial yet–but that’s coming. We now have sent the script to the studio and we’ll be assembling that soon.

I do want to mention one thing that we think is interesting, and we see in almost every training we do. Nearly every time, more than half of the attendees at our trainings are female. Based on what you read about women falling out of the pipeline in science, you’d think there would be no way we’d even get 50%. But generally it is more than half women in these trainings. (We have the data if anyone can think of a way we can use that to get a grant )

Our current theory is that women are more likely to admit they could use the training (something like asking for directions…you know…?).  Or do men prefer documentation? We don’t know. What’s your theory?

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

Recently the Galaxy team hosted a developer conference.  As I was following the tweets I was very intrigued by the topics–and the attendees certainly seemed excited by the presentations.

If you want to see what’s going  on out there  with various installations of Galaxy and the applications that are being employed, check out the slide collection from the conference here:

http://bitbucket.org/galaxy/galaxy-central/wiki/DevConf2010

If  you don’t  know much about Galaxy yet, check  out our introductory tutorial on it, sponsored by the Galaxy folks and freely available: http://www.openhelix.com/galaxy

Sorry, this was mostly over the weekend–but there’s still some more today.  But the Galaxy team had a conference that brought together a lot of people running local installations of Galaxy for various purposes.  You can see the agenda here:

First Galaxy Developer Conference

There are slides, notes, and twitter comments from attendees if you are interested.  The hash tag #gxy will bring up the links. There is still another session today so there may be more activity.

For those of you who don’t know why Galaxy is so cool, check out our introductory training on Galaxy, freely available because it is sponsored by the Galaxy project team.  That will give you the foundation.  What these developers are doing is taking that foundation and customizing it for local needs and the tools their users want to access, and generate workflows, and share analysis, etc.

Or go directly to Galaxy here: http://www.galaxyproject.org

I’d like to point out the new NCBI Education page. There is a lot there that you might want to check out. NCBI will be, starting this fall, offering a series of two-day training courses they are calling Discovery Workshops. Two years ago they ended the NCBI Field Guide workshops, so this seems to be a welcome change.

There are also webinars. Our research suggests that webinars are not particularly popular, so I’m curious how these turn out. There are also ‘how-to’ guides, documentation, community, teacher resources. It’s quite a nice site with lots of things to check out.

I’d also like to point out the “recommended links” section. There are lots of links to additional educational resources like the Cold Spring Harbor’s Dolan DNA Learning Center and much more. And, incidentally , a link to our own free tutorials which was very nice to see. You might want to check those out, we have over 10 including PDB, SGKB, UCSC Genome Browser, Galaxy, several model organism databases, and more.

We know there are a number of different ways that scientists and students become familiar with genomics software.   Some of it comes from the traditional publication routes–like the very handy NAR Database issue.  Or like the Current Protocols papers we’ve done recently.  We have these online tutorials that people use in various ways: some teach themselves by watching the video and working the exercises, some download the matching slide sets and run local workshops (our catalog: some are free/sponsored and green icons indicate that; red indicates subscription required). Librarians are using them to become “embedded” in courses in some cases.

A less-well-known type of material we have is the Quick Reference Card.  These are printed cards with URLs, hints, tips, definitions, shortcuts–for stuff that you may want a quick reminder of: where a feature is located, or how to use it.  People who run the local workshops will sometimes write to us to get a set for their courses.  They are great to give out at conferences to raise awareness of the software.

We have these cards for several resources that we also have free sponsored training videos + slides + exercises with: UCSC Genome Browser (2 cards–intro and table browser); Galaxy, and our newest: RCSB PDB and SGKB.  You can go to this form and order them, and we’ll send them out.

I bring this up today because we just received word from Ensembl that they have created a card that we can distribute as a PDF.  You can print it up and put it on the wall near the computer as a handy reminder of some features and tools at Ensembl.  Click the image to download the PDF, or go directly to the link below.

Summary:

Order OpenHelix printed cards for resources: http://www.openhelix.com/cgi/qrcOrder.cgi

Ensembl PDF card download: Ensembl_card_march2010.pdf

I’m deeply immersed in a new project right now, so my blogging has been light of late.  But in lieu of that–you can check out a new paper on Galaxy that’s just come out!  We were approached by the Current Protocols in Molecular Biology team last year because they saw the need for works that were aimed at the folks who aren’t already in bioinformatics.  So we crafted a couple of papers designed to be useful for people who are doing benchwork and need to accomplish things with bioinformatics tools, but don’t need to be experts or coders.

The Galaxy paper has now been published, and you can check it out here: (subscription required)

Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists

I think it is very effective at step-by-step guidance on some tasks that scientists are likely to need, if I do say so myself as one of the authors .  There are also accompanying screen casts for additional assistance.   You can also see our free tutorial sponsored by the Galaxy team for an overview and orientation of Galaxy as well.

As Trey posted last week in part I, we’ve been doing tips-of-the-week for two years now. We have completed over 100 little tidbit introductions to various resources*.  At the end of the year we are doing a summary post to collect them all.  If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

I’ve got the second half of this year to summarize–July through December 2009. Check them out!

July 2009

7/1  UCSC wiki annotations UCSC has created a way for anyone to add annotations to their genes of interest using a wiki.

7/8  CellMiner from NCI A relational database for cancer cell line data.

7/15  ENCODE data at UCSC The Data Coordination Center, or DCC, for the human ENCODE data is introduced, with guidance on how to access ENCODE data in the UCSC Genome Browser.

7/22  It’s a duplicate Check out Deja Vu, a program to assess scientific abstracts for similarity, including duplication or possible plagiarism events.

7/29 VirusMINT The Molecular Interaction Database that we love added a component for Virus protein interactions.

August 2009

8/5  Genomic Encyclopedia of Bacteria & Archaea (GEBA) This piece on the strategy of choosing new genomes to sequence was introduced in August.  If this is of interest to you, also check out the recent publication about this project that we talked about here.

8/12  NCBI’s New BioSystems Resource Wherein NCBI takes on the storage and representation of biological network data.

8/19  PLAN2L for Arabidopsis literature A helpful tool for literature searching for Arabidopsis.

8/26  Acytelome, String and a new database An introduction to the Phosida database, for phosphorylation and acetylation information.

September 2009

9/2 A mouse for all reasons Learn about the knockoutmouse.org site, which provides information and reagents for generating knockout mice.

9/9  TARGeT A resource for identifying transposable elements and genes relationships from sequence submissions.

9/16  The National Center for Biomedical Ontology This central repository for Ontologies can be really helpful for bioinformatics software project developers.

9/23  JBrowse, a game changer? A look at a new strategy in genome browsing software.

9/30  Finding the right genomics resource This is a quick introduction to OpenHelix’s own new interface for searching for training movies and materials!

October 2009

10/7  NCBI Makeover! The overhaul of the NCBI interface–with a walk through memory lane at some of it’s previous incarnations–is provided.

10/14  Getting flanking sequence A quick look at how to use Galaxy to obtain adjacent sequences, which is a question we are asked frequently in training situations.

10/21  SwissVar, a New Genotype-phenotype Resource from SIB Explore ‘a portal to Swiss-Prot diseases and variants.’

10/28  Sol Genomics Network Do you like tomatoes, eggplants, potatoes, peppers, and other members of the Solanaceae? If so, check out this resource.

November 2009

11/4  CHOP CNV database If you are curious about copy-number variations, be sure to explore the collection at CHOP.

11/11  GeVo and Genome Comparison A nifty tool for genomic comparisons.

11/18  FABLE, text mining for literature on human genes A literature mining resource to improve you searching.

11/25  Got tips for us? We opened the floor for suggestions of tools to look at as we celebrated the Thanksgiving holiday.  We’ll still take suggestions–we love to explore new resources!

December 2009

12/2  RCSB PDB Comparison Tool Compare sequences for structural similarities with this handy widget.

12/9  GRAIL for prioritizing SNPs Use a list of SNPs to identify associated genes, and then sweep the literature for leads on the processes that might be involved.

12/16  GenomePad Check out this very cool iPhone app for exploring the UCSC Genome Browser.

12/23  Tip of the Week: Year (2nd!) of Tips for the first half of the year’s summary of tips.

*for the vast majority of resources we introduce in our tips, we have no financial relationship with the provider or developer. The ones we do are listed here.