The OpenHelix Blog

Recently while watching the #bioinformatics tag on Twitter I saw Khader Shameer mention Caleydo.  I was instantly hooked at the very clever visualization strategy that they are using to provide more surface area for examining the data you are interested in viewing.  Their specific topics are pathways and gene expression, but it got me thinking about various data types that I would like to see connected in this way.

To skip right over to Caleydo and start trying it out, go here: http://www.caleydo.org/

Caleydo delivers a 3D representation of the expression and pathway data.  The main user interface has an area that is a box.  They call it a bucket, but in my head buckets are round, so I think of this as a box.  On the floor of the box you have a graphic.  But because you also have 4 interior surfaces of the box you have 4 more places to display and link the data.  You can have a heat map microarray representation on one side, and various pathways associated with the genes in that microarray on the other sides.

There’s a short systems biology Application Note in Bioinformatics that describes the framework and gives an overview of the tool.  But there’s also a more detailed paper over at their publication site that will get you started (that 2010 paper for the Visualization conference in Taipei).

My computer is a bit underpowered, but I was able to load their webstart version and begin to look around.  They provide some sample data you can select and examine.  For the movie this week, though, I was unable to load that and run the recording software at the same time.  So mostly it’s an introduction to the concept and the site.  You’ll have to go over and load it up yourself to try it out.  If the webstart version doesn’t work for you, there are a couple of other download options for different platforms.

The Caleydo team has also done a YouTube overview of the features that you can examine.

http://www.caleydo.org

So try out this visualization strategy and see what you think.  I really like the concept.

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Streit, M., Lex, A., Kalkusch, M., Zatloukal, K., & Schmalstieg, D. (2009). Caleydo: connecting pathways and gene expression Bioinformatics, 25 (20), 2760-2761 DOI: 10.1093/bioinformatics/btp432

From a systems biology mailing list I’m on, I got this announcement. As I no longer qualify as…ah…young…apparently…I’m going to pass this along to young investigators interested in this area. Personally if I was starting out a career in biology/bioinformatics/genomics at this time I would move in this direction. There’s some very exciting stuff developing there, and it looks to me like there’s room to find a niche.

Anyway, here’s the announcement, reprinted with permission. There’s no web site yet, the tell me they’ll let me know when one is live.

The European Commission is funding the FutureSysBio project, a coordination and support action that aims at shaping and predicting the future development of the field Systems Biology. We are now planning for the first focused workshop, which will discuss the topic “What is needed for SysBio to enter the clinic”?

Focus will be very much on open discussions and brainstorming around specific topics and questions The outcome of the workshop will be documented and disseminated in various reports to different target groups (funding agencies, industry, the scientific community, media, the general public) and possibly as a publication in a suitable scientific journal. Social events will also be organised.

The workshop will take place in Gothenburg, Sweden, with arrival in the morning of Nov. 19 and departure in the afternoon of Nov. 21.

We are looking for ten young scientists (max five years after PhD) who would like to actively participate in the workshop. Please send by e-mail (martin.markstrom[AT]gu.se): (i) a one-page letter of application describing your interests and why you would like to participate; (ii) a one page CV; (iii) the name and email address of a senior scientist at your department who can act as your reference.

Your application should reach us by mail no later than Oct. 20. Successful applicants will be notified by Oct. 24. The FutureSysBio project will cover participants’ costs as far as they are within the usual range (economy class ticket).

With the best wishes,

Stefan Hohmann and Jens Nielsen

Check it out. Pass it along to interested colleagues.

We are thinking quite a bit about pathway tools these days. I got a jolt of input on them from the ICSB meeting recently, too. As I continue to progress through my meeting notes I’ll be checking out more tools and writing about them.

One of the things that seemed new and important (well, to me at least) was the first release of a set of standards for drawing pathway diagrams. During this meeting they announced the release of 1.0 of the SBGN notations (also known as Level 1; more levels are anticipated as this progresses). SBGN is Systems Biology Graphical Notation. You can access the SBGN site here: http://www.sbgn.org/

The idea is that if we can standardize our representations of pathways we can all be sure that the meanings are the same for arrows, and boxes, and so on. For example, if I draw a pathway with an arrow, my arrow means the same thing as your arrow in your pathway diagram.

What the SBGN team says on their homepage:

SBGN defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules defining their use and how diagrams are to be interpreted.

So this is kind of like Gene Ontology for systems and pathway diagrams. Not only is it increasing the clarity of the diagrams, it will guide software development so that software for generating diagrams and analytical tools can work in this framework as well.

There are examples on the web site. Check out the document on the specifications (a big PDF), too–lots of detail on what, how, and why this is important. They want feedback on this. You can also check out the associated SBGN wiki with more details and the SBGN forum for interaction with the team.

Still enjoying the ICSB meeting, and it is a gorgeous fallish morning in Göteborg. What a great city and terrific people here. Not entirely sure I want to come home….

My brain is approaching “full” already, and there are still several days to go. I’ll have a lot of tools to talk about in the coming weeks as I check more of them out. But I wanted to talk about a couple of neat tools that I have heard about so far. First–CellDesigner 4.0, that I mentioned the other day, was a good choice of tutorials to attend for sure. You can access their tutorial material here. Turns out they are also about to release a web-based version of this that will be a collaborative community editing tool for networks and pathways. It is called Payao–which I’m told means a type of “fish-aggregating device” according to their poster. I was unable to catch the poster authors so far to discuss it further, but it looked like a neat tool. I can’t find a release on the web yet and there was no URL on the poster. I’ll try to track them down again today.

Update: Found it here http://celldesigner.org/payao/payaopreview.html

Another fun tool (which I haven’t had a chance to use much yet) is BioMyn. The idea behind BioMyn is that it is something like a Google search for systems biology and other relevant biological data types. It aggregates a lot tools into a single search, here’s a partial list: ensembl, MINT, GAD, HPRD, Corum, InterPro, PDB, OMIM, GO, Reactome, KEGG, UniProt, HiMap, IntAct, GNF, and DIP. I spoke to Fidel Ramirez, the creator, about this tool and he was very eager to have users and feedback on this new beta phase. He was saying that people have suggested the results link should be re-organized a bit. If you do a search you get a list of results and some context. The link at the top goes to your “best” resource hit–leaving BioMyn. But if you click the link at the bottom of the result ( View all annotations for …) you go to the aggregated results in BioMyn. Organized into a collection of data in tabs, you can find a wealth of information on this gene. You can find gene links, of course, but also diseases, pathways, interactions, GO terms, and on and on. Anyway–check it out. And keep in mind it is beta. Feel free to offer feedback here and I will pass it along to the developers–they don’t have a feedback link on the site yet. But they do have a blog, I suppose you could put comments over there. In fact, I’ll suggest that to the team today if I see them.

I’m in Göteborg today, at the ICSB International Conference on Systems Biology. I’m taking a couple of the tutorials today. My first one is on the Edinburgh Pathway Editor or EPE (description of this can be found in this PDF of the session). They have made available a 2.0 version for the attendees here. I’m eager to learn more about this.

The next session I signed up for is CellDesigner 4.0. You can learn more about it from the session PDF here.

Both of these tools require downloading and installation. We usually focus more on web-based software, but these systems biology tools often require you to install and run it locally. You can get the software directly from these sites:

Edinburgh Pathway Editor: http://www.bioinformatics.ed.ac.uk/epe/index.shtml

CellDesigner: http://celldesigner.org/

Have fun! I expect I’ll post more thoughts on them after I have had a chance to dive in and swim around some.

The Jackson Lab courses are really terrific–I took a couple of them while I was up there for my post-doc. This announcement just came over the mailing list and I thought I would pass it along. I’m thinking a lot about systems biology and the tools for it right now (more details on that later), and so I’m going to need more people generating data so I can play with the tools. And September in Maine is a nice time, btw:

Applications continue to be accepted for the Short Course on Systems Genetics being held September 23-29, 2008 at The Jackson Laboratory in Bar Harbor, Maine.

This one-week course will cover computational and experimental approaches to genetic studies that utilize the whole genome approaches. Lectures and computer workshops are designed to accommodate students with a wide variety of backgrounds. Biologists seeking to gain a deeper understanding of statistical and computational methods as well as quantitative scientists desiring exposure to biological problems are welcome. Topics to be covered include genetic mapping, gene expression microarray analysis and computational modeling of complex systems.

For more information, including the course schedule and application instructions, please visit http://courses.jax.org/2008/systemgenetics08.html

The tourists are mostly gone at this point, and the town is still running. Good time to visit Bah Hahbah.

http://courses.jax.org/2008/systemgenetics08.html