First release of LibSBGN

February 10th, 2011

After months of work, last week we finally released the first version of LibSBGN.

LibSBGN logo

So what is LibSBGN? The Systems Biology Graphical Notation (SBGN), is a standard for drawing pathways. It prescribes exactly how to draw a biochemical reaction, how one can display the effect of heat on protein degradation, or how you should present the formation of a protein complex. It’s unambiguous: no matter how complex the drawing gets, it can be interpreted in only one way. SBGN is the result of many discussions, arguments and debates, over the course of several years and it’s therefore really well thought out.

Good software support is essential to make SBGN succeed as a standard. LibSBGN was created in an attempt to encourage uptake. As the name implies, LibSBGN is a software library that should make it easy to incorporate SBGN in pathway tools.

LibSBGN is only a software component, it’s not a ready to use end-product by itself. So this announcement is probably only interesting to bioinformatics developers. Nevertheless, I hope that it will soon lead to an increased uptake of SBGN in pathway tools, which should benefit end-users of those tools as well.

LibSBGN is already supported by a few applications, including of course PathVisio. To make sure that it works exactly the same in each tool, we’ve created a comparison gallery, containing several test-cases rendered by each tool. All the diagrams should look exactly the same for each tool. This comparison page has proven tremendously useful to check for bugs and misunderstandings.

This is only the first release, there is still a lot to do. This first release only supports a part of SBGN called process description (PD). The coming months will see lots of work on the remaining parts of SBGN, entity relationships (ER), and activity flow (AF). And after that we’ve planned more features, such as validation rules and file format conversion.

This is the first tangible result from something that was set in motion at a meeting in Wittenberg. LibSBGN community: thanks for your hard work and congratulations on this first milestone.

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Spaghetti DNA

January 30th, 2011

This is in the category “parallels between life and computers”.

DNA is said to contain the instructions to build an organism, just like software contains instructions for a computer. Poorly structured software is sometimes called “Spaghetti Code” because it’s such an intangible mess. What about the structure of DNA? Here is a nice quote from the linux kernel mailing list (link):

> Human communication methods are all buggy as hell :)

Not to mention that they are slow, inefficient and ambiguous.

But wht did you expect? The original authors of the code are long gone and
maintenance is done by newcomers who are patching the code bit by bit. What
you get from such a development model is pretty predictable: ~1 billion years
old spaghetti DNA that no-one truly understands.

Evolution may be a “poor development model”, but at least DNA has seen billions of years of debugging 🙂

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Oracle versus Google

August 20th, 2010

A while back I wrote rather optimistically that I expected Oracle to play nice with the open source community

“I don’t see why Oracle won’t be able to keep MySQL open and still have a nice profitable business model.”

However, all that seems rather less likely, now that Oracle is suing Google over patent infringement in the open source Android platform.

Here is a great point of view from a Java developer on this lawsuit. Not only it explains what the suit is all about, but also gives historical perspective, how Java got into this mess in the first place.

From that link:

“Android actually *was* a great platform that supported existing Java developers and libraries incredibly well (without actually being a Java environment), and for the first time there was a serious contender to “standard” Java that Sun had absolutely no control over.”

and:

“If for nothing else, Jonathan Schwartz will be remembered as the man who broke open the Sun piñata, simultaneously releasing more open-source software than any company in history and killing Sun in the process. Either Jonathan had no “step 2″ or the inertia of a company built on closed-source products was too great to overcome. In either case, by spring of 2009 Sun was hemorrhaging”

It’s long but well worth a read if you are concerned about the future of Java.

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Going to COMBINE 2010

July 31st, 2010

COMBINE 2010 is a meeting about all systems biology standards: SBML, SBGN, BioPAX, … etc. It’s from October 6 to 9 in Edinburgh, just before the ICSB conference.

Registration just opened, I’ve already signed up.

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SBGN 5.5 Hackathon writeup

April 25th, 2010

The goal of Systems Biology Graphical Notation or SBGN is to define a set of standard shapes for things like reactions, enzymes, genes, metabolites, compartments etc. For example, here is the reaction that takes place in your body after an alcoholic beverage, using SBGN notation.

Alcohol dehydrogenase as SBGN diagram

The SBGN community organizes regular meetings or “hackathons”, where specs are discussed and new SBGN-related software is presented. This year I was present at the meeting held at Wittenberg in Germany (where you can still find the church door where Luther pinned his 95 theses). Here is my writeup, by no means complete, just a collection of impressions.

Vanted SBGN-ED
In the category SBGN-related software, Tobias Czauderna demonstrated SBGN-ED,  a new plugin for Vanted that lets you create diagrams in SBGN format. Especially interesting is the nice validator that can tell you if you drew something that is not allowed by the SBGN specifications. A very complete SBGN editor and probably one of the nicest out there. No link yet, but there will be a publication very soon.

Vanted BridgeDb plugin
Unfortunately a few presentations had to be canceled the first day due to the volcanic ash that was plaguing the European skies. To fill the gaps in the agenda, we just started hacking on random stuff. One result of this was a Vanted BridgeDb plugin that I made together with Christian Kuklas. Christian immediately found a number of bugs and requested new features in BridgeDb. There is not yet an easy way to install the plugin, but if you’re interested you can play with the source code

SBGN Exchange format
The second and third day, most participants managed to overcome the disruption of the air traffic and join the conference. Besides discussion on the planned next release of SBGN, there was another important topic: LibSBGN.

SBGN currently only exists as a specification of glyphs and symbols and what they mean, there is no computer file format. But there are now several software packages out there that deal with SBGN, and they need a standard exchange format to work together.

The existing standard file formats for pathways, SBML and BioPAX, do not store  layout information, i.e. they do not store the position of the elements of a diagram. According to the SBGN spec, layout information does not carry any meaning. Biologically the diagram means the same thing, no matter if elements are arranged vertically, horizontally, in a circle, or in random order. So you would think there is no problem.

But as it turns out, it’s exactly the layout information that has to be exchanged between pathway software. It turns out that a good pathway layout is really hard to do automatically, so once you have painstakingly defined a layout you want to preserve it. So weirdly enough we want an SBGN file format to exchange information that is not part of the SBGN spec at all.

Because there is no standard, the current tools all defined their own ad-hoc file format out of necessity. The lack of a standard file format is really becoming an impediment to cooperation. There has been a lot of talk how this should look like, XML? DTD? GML? Object model? But in my opinion it doesn’t matter too much in the end, you just have to make a decision and stick with it. We’ve been able to turn a lot of discussion into tangible results in the form of a new SourceForge project, and uploaded some small samples and the beginnings of an XML Schema definition. Hopefully we can keep the momentum and get it mostly done by the next SBGN meeting.

jSBML
Not related to SBGN directly, but I found it interesting nontheless: A new java native library for SBML is being developed called jSBML. There already existed a library called libSBML, but it’s written in C++. Because LibSBML was considered a “good-enough” solution for java programs, the SBML community for a long time resisted the notion of a native java library. But it turned out that many SBML-based Java projects were actually developing their own native library anyway. Ironically,  the tendency to avoid duplication of work actually led to multiple incomplete projects that all duplicated each other. Sometimes it’s best to accept reality.

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WikiPathways Curation Jamboree Evaluation

April 16th, 2010

WikiPathways content is growing nicely, but it’s not growing like one of those nice exponential curves that you see in the first slide of almost every bioinformatics presentation nowadays. We want exponential curves in our presentations too, dammit, so we want to get more people actively involved.

A big challenge for WikiPathways is to get people to take the first step, to get them over that initial hump and actually start participating. Certainly a lot of people are very interested in WikiPathways, but there is some hesitation to just start working on the content. It’s something we have to work on. Besides clearing technical hurdles, we try to gently help people, simply to get started.

As an experiment, we organized a dedicated curation jamboree, a focused effort to get together and crank through a list of curation tasks. We prepared documentation, contacted several mailing lists and harassed all our colleagues. We also put together a special chat channel where newcomers can get instantaneous contact and answers to quick questions. This event happened for two days in February.

So, was it a success? Yes, if you look at edit activity. Thomas made this graph of the number of pathways tagged with either “needs reference” (for pathways that don’t have any literature references) and “missing description” (for pathways that don’t have a nice description text). As you can see, the numbers dropped quickly during the two days of the curation event, by at least 25%. (ignore the initial jump in the blue line, that’s due to a bug in the data collection script). WikiPathways gained a lot of curated data in a short period of time.

Numbers of pathway with a curation tag over time

The most active contributors were the usual suspects: Thomas, Alex, Kristina and me, the core WikiPathways team. But you can see in the graph below that other people joined in as well. Even if they did only a few curation tasks, that’s good  enough. The most important thing is to get people to take the first step. So the graph below is misleading: participating really is more important than winning.

Number of edits per user

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That’s Great, Now Please Fix OpenOffice.org

April 8th, 2010

Did you hear about the OpenOffice.org mouse? It’s a mouse that has no less than 18 buttons. From the press release:

“With a revolutionary and patented design featuring 18 buttons, an analog joystick, and support for as many as 52 key commands, the OOMouse is intended to provide a faster and more efficient user interface for most complex software applications than the conventional icons, pull-down menus, and hotkeys presently permit.”

This is the same logic that brought us the 5-blade razor. Somebody please smack these people with a copy of The Design of Everyday Things. Why would anybody want such a complicated thing? Beginning users will not be interested in memorizing 18 unmarked buttons. And for advanced users, ordinary keyboard shortcuts are much more effective anyway, because they will prefer to keep their fingers near the home row (the row from “asdf” to “jkl;” – touch typists are trained to put their fingers there at all times). For maximum speed, you want to move your hand away from the keyboard as little as possible.

This is even more ironic when you consider that the OpenOffice.org suite, in spite of all its open-source karma, is still full of tiny annoyances. What OpenOffice.org needs now is a focus on user-friendliness, not a mouse that looks like the console of a nuclear power-plant.

Just a tiny example. I’ve used MS Word a fair bit and I’ve learned a lot of handy keyboard shortcuts. Just try this: if you want to change the style of a paragraph, just press Ctrl + Shift + S, and start typing the name of the style you want. The same trick works with Ctrl + Shift + F for font and Ctrl + Shift + P for font size (points). If you have to do this a lot, this shortcut is a great time saver. I haven’t been able to find any equivalent shortcut in OpenOffice.org. Is that the reason why we need an 18-button mouse now? Can’t we just fix the software itself?

I wonder why OpenOffice.org allowed their name to be used for such a weird project. I fear that this will only re-enforce the stereotype that open source software is never user-friendly.

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BridgeDb: now also with metabolite identifier mapping

March 25th, 2010

Ha, fooled ya! BridgeDb has been able to deal with metabolite identifiers since the beginning. But mapping genes is such a common problem that metabolites aren’t getting any attention. Nearly all the code examples that we have thus far are with genes.

Somebody on the mailinglist asked for an example with metabolites. Well here you go, you’ll see it’s really easy. This example takes the ChEBI identifier for methionine, and looks up the corresponding PubChem identifier.

// Using the BridgeRest webservice as mapping
// service, it does compound mapping fairly well.
// We select the human species, but it doesn't really
// matter which species we pick.
Class.forName ("org.bridgedb.webservice.bridgerest.BridgeRest");
IDMapper mapper = BridgeDb.connect(
    "idmapper-bridgerest:http://webservice.bridgedb.org/Human");

// Start with defining the Chebi identifier for
// Methionine, id 16811
Xref src = new Xref("16811", BioDataSource.CHEBI);

// the method returns a set, but actually there is only one result
for (Xref dest : mapper.mapID(src, BioDataSource.PUBCHEM))
{
    // this should print 6137,
    // the pubchem identifier for Methionine.
    System.out.println ("" + dest.getId());
}

Compile this example with org.bridgedb.jar, org.bridgedb.bio.jar and org.bridgedb.webservice.bridgerest.jar in the classpath, which can be downloaded from http://bridgedb.org/data/releases/

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Google Summer of Code 2010

March 18th, 2010

Yay! It’s official, we’re going to be in the Google Summer of Code again this year. Our application as a mentoring organization was just accepted. Cytoscape, PathVisio, WikiPathways and even BridgeDb are all joined under the GenMAPP umbrella organisation. Unfortunately I don’t have time to mentor again, so I’ll be watching from the sidelines this year. But I do want to encourage students to apply.

Students from all nations, we want to hear from you! If you’re interested in developing open source bioinformatics software, please send us a proposal. Check our ideas page, write a proposal and send it to our mailinglist. You have a chance to gain valuable development experience and earn a little money at the same time. The earlier you contact us, the better your chances.

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The Downside of Modularity

March 13th, 2010

I’m a big fan of modularity. I’ve even got a modular system in my living room. It consists of the following modules:

  • One module that converts a digital signal to a two-dimensional picture.
  • One module that reads a rotating plastic disk with a laser and produces a digital signal.
  • One module that gets a digital signal from a socket in the wall, stores it temporarily on magnetic disk, and sends it out again upon request.
  • One module that generates a digital signal based on a simulation of a virtual world, with which I can interact in real time using motion and pressure sensitive input devices.

In case you hadn’t guessed already, I was talking about my TV, DVD player, Hard-disk recorder, and Game Console.

Imagine if all of this came in one device. A TV+DVD+HDR+Console-in-one. Imagine what it would cost. If only one part broke, I would have to get everything anew. I would never be able to move it abroad, because the HDR is tied to my cable provider. I would never be able to get the games that do not involve Italian plumbers.

But to be fair, there are also disadvantages to modular systems. Just take a look at the remote control that comes with it:

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