This message constitutes notice of a Last Call for comments on XEP-0244 (IO Data).
Abstract: This specification defines an XMPP protocol extension for handling the input to and output from a remote entity.
URL: http://www.xmpp.org/extensions/xep-0244.html
This Last Call begins today and shall end at the close of business on 2009-09-01.
Please consider the following questions during this Last Call and send your feedback to the standards @ xmpp.org discussion list:
- Is this specification needed to fill gaps in the XMPP protocol stack or to clarify an existing protocol?
- Does the specification solve the problem stated in the introduction and requirements?
- Do you plan to implement this specification in your code? If not, why not?
- Do you have any security concerns related to this specification?
- Is the specification accurate and clearly written?
Your feedback is appreciated!
There remains quite a lot to do, and you are more than welcome to join in the project. There is a Java library and we’ve integrated the specs into Bioclipse and Taverna (see Details behind the “Calling XMPP cloud services from Taverna2” ), but there is no support for BioCatalogue yet, and no libraries for other programming language yet.
]]>Update: OpenHelix discusses the matching genome browser, and indicates that hundreds of genomes are actively being studied. The group where I work recently bought a 454 (reg needed, it seems) and participates in the race. Nibbles links the cork event to square peas… but my biological background prohibits me to see that link…
]]>Well, Christoph has done many other Open Source and Open Data stuff, including the NMRShiftDB, Bioclipse, and Seneca, a tool for computer-aided structure elucidation (CASE). The scientific impact for Christoph’s work is considerable. When I realize that much of his past work was setting out foundations, and that these foundations have found the be solid, I am happy to hear that he can now start to apply his work to life science problems, where current methods are failing.
Christoph, cheers!
]]>When we were beta-testing [two new bioinformatics programs] on microarray data, a frustrating problem occurred repeatedly: Some gene names kept bouncing back as “unknown.” A little detective work revealed the reason: … A default date conversion feature in Excel … was altering gene names that it considered to look like dates. For example, the tumor suppressor DEC1 [Deleted in Esophageal Cancer 1] was being converted to ‘1-DEC.’ Figure 1 lists 30 gene names that suffer an analogous fate.
…
There is another default conversion problem for RIKEN clone identifiers identifiers of the form nnnnnnnEnn, where n denotes a digit. These identifiers are comprised of the serial number of the plate that contains the library, information on plate status, and the address of the clone. A search … identified more than 2,000 such identifiers out of a total set of 60,770. For example, the RIKEN identifier “2310009E13” was converted irreversibly to the floating-point number “2.31E+13.” A non-expert user might well fail to notice that approximately 3% of the identifiers on a microarray with tens of thousands of genes had been converted to an incorrect form, yet the potential for 2,000 identifiers to be transmogrified without notice is a considerable concern. Most important, these conversions to an internal date representation or floating-point number format are irreversible; the original gene name cannot be recovered.
Is this the article that made all bioinformaticians turn to R?
]]>I have no idea if this site will be a success, but at least it has the right ingredients: tags, flash movies, clean UI, a blog to monitor technological changes and improvements, and a page to request screencasts (with voting). What I only miss is a one summary page for each screencast to which I can easily link, for example for my del.icio.us account.
]]>Below is a list of bioinformatics programs which are free for academic use, but not open:
And this not even includes the many websites which do not offer the software behind them. And these programs cover several steps in the whole homology modeling process. Open source homology modeling is not possible at this moment :(
But, on the bright side, there are already some open source programs involved too:
And protein structure viewers is hardly a problem at all; several open source viewers are available, among which Rasmol, PyMOL and Jmol.
In other words: we might not want to look at bioinformatics too much.
]]>I have my laptop with me, and, of course, the Blue Obelisk Live CD 2 on which the mouse now actually works. Bioclipse 0.9.1 does not work, though; will report that bug later.
My work schedule for the train ride:
The ‘source code’ aspect is the interesting thing of this new journal. The editorial board set the aim to publish source code for distribution and use in the public domain in order to advance biological and medical research. And, in a bit more detail, they list the following goals:
This comes close to what open source is trying to achieve too, but I do not differences. For example, the announcement mentions the public domain (see the Wikipedia entry). I tend to be a bit confused by the use of this term: to me the public domain is where things end up after copyright claims have ended, and everyone is free to do with it whatever he wants, and, very important in this case, that open source software is not in the public domain. Do they mean that they will not allow open source in the new journal?
I also wonder wether we need a journal like this? Open source projects often have other resources available that serve as repository (e.g. SourceForge ), and the use version control systems as repositories (like CVS, Subversion) is widespread too, which takes care of the historical reflection. Indeed, many open source software is already published in other journals.
The process of picking the journal to submit to, often involves looking up the journals impact factor. Is this new journal expected to get a high impact factor? How many people will regularly read the journal? Will it be read by the right audience, or just by fellow bioinformaticians?
Though I have my doubts about the success of this journal, I am looking forward to the first issue!
Update: Pedro pointed me to the About page of the SCFBM, giving details on the types of articles taken into consideration.
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