Archive for March, 2012

Drawing Formulas

One of those nifty little tools that just make life easier: WebEquation by VisionObjects.

Just draw your formula, and it returns the corresponding LaTeX or MathML code. For me, it works great with a cheap graphics tablet, feels a bit more cumbersome (but ok) with the mouse – but still waaay better than messing around trying to convince LaTeX to let that darn’ formula say what you really want it to say. As an example, I just did Euler’s identity in a couple of seconds. For all of us who don’t do this on a daily basis 😉

Found via SchockWellenReiter.



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Europe’s science cloud: Helix Nebula

… a consortium of leading IT providers and three of Europe’s biggest research centres (CERNEMBL and ESA) announced a partnership to launch a European cloud computing platform. ‘Helix Nebula ‐ the Science Cloud’, will support the massive IT requirements of European scientists, and become available to governmental organisations and industry after an initial pilot phase.
The partnership is working to establish a sustainable European cloud computing infrastructure, supported by industrial partners, which will provide stable computing capacities and services that elastically meet demand.

Building an efficient scientific cloud infrastructure in europe is a good thing, considering the onslaught of data from genomics, high-energy physics and sattelites. But I somewhat can’t shake off the uneasy feeling that the big-science flag-ship projects don’t leave any room for grassroots developments anymore, i.e. movements like the WWW when it took off in the mid-nineties. Along these lines, I’d rather (or at least equivalently) see the LinkedOpenData (as advocated by Tim Berners-Lee for several years) agressively being pushed forward and funded appropriately, the pay-offs are hard to (over-)estimate. But anyway, here are some links to make up your own mind:

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Visualizing Biological Data

The VizBi-2012 Conference took place in Heidelberg this week – unfortunately I couldn’t attend it. Nevertheless, I received a bit of summary and feedback: The talks will be made available online, I am looking forward to check out a few of them (i.e. Jim Robinson, Jernej Ule). Ivet Bahar (ProDy) and Valerie Daggett (Dynameomics) gave an interesting overview on Molecular Dynamics.

The conference was preceeded by a several tutorials on Monday. Among them on was one on Processing.js (which has been mentioned around here a few times before) and one on D3.js. Both are based on JavaScript and generate cool Visualisations for the Web. D3 only recently got onto my radar, it’s document driven approach seems quite powerful. So it’s definitely worth a look –

see some more examples (like the force-directed layout on the right) on and the workshop slides can be found at

Thanks to to Corinna Vehlow for feedback!

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Molecular Interaction Exchange

The International Molecular Exchange Consortium IMEx is the latest effort of data-providers to integrate Protein-Interaction Data –

IMEx provides

  • A non-redundant set of protein-protein interaction data from a broad taxonomic range of organisms
  • the data in standards compliant download formats (MITAB or PSI-MI XML 2.5)
  • Expertly curated from direct submissions or peer-reviewed journals to a consistent high standard.
[ … aiming to … ]
  • Develop and work to a single set of curation rules when capturing data from both directly deposited interaction data or from publications in peer-reviewed journals
  • Make these interaction available in a single search interface on a common website
  • Make all IMEx records freely accessible under the Creative Commons Attribution License

If you’ve been looking for that one-stop shop for getting a representative dataset of Protein-Protein Interactions, this just looks like it. There is an overview available on youtube (see below)

… and a training course on “Networks and Pathways Bioinformatics for Biologists” will take place at EMBL-EBI in May.

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