MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'peanutbutter' source. Wed, 19 Nov 2008 22:52:10 +0100 http://peanutbutter.wordpress.com/2008/10/30/the-triumvirate-of-scientific-data/ In a recent Nature editorial entitled Standardizing data,  several projects were highlighted that are forfeiting there chances of winning a Nobel prize (according to Quackenbush) and championing the blue collar science of data standardization.in the life-sciences. I wanted to take the article a step further highlight three significant properties of scientific data that I believe to be fundamental in considering how to curate, standardize or simply represent scientific data; from primary data, to lab books, to publication. These significant properties of scientific data are the content, syntax, and semantics, or more simply put -What do we want to say? How do we say it? What does it all mean? These three significant properties of data are what I refer to as the Triumvirate of scientific da... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1920884 Thu, 30 Oct 2008 14:39:10 +0100 1920884 http://peanutbutter.wordpress.com/2008/09/09/the-uk-e-science-all-hands-meeting-2008/ Image via Wikipedia The UK e-science All Hands Meeting (AHM) 2008 is currently underway in Edinburgh. I will not be taking notes via this blog, instead I will be microblogging via my FriendFeed. Other delegates already on the FriendFeed band-wangon are Daniel Swan and Jean-Claude Bradly. Hopefully by the end we will have some more e-science FriendFeed converts. I will also be tagging AHM relevant posts via delicious using the tags e-science+AHM+ 2008. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1775481 Tue, 09 Sep 2008 10:34:41 +0100 1775481 http://peanutbutter.wordpress.com/2008/09/05/mged-by-ally/ Ally has completed her comprehensive review of the 11th MGED Society meeting - I feel as if I was actually there.  She also won 3rd place in the best poster competition which she presents SyMBA. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1768773 Fri, 05 Sep 2008 12:09:56 +0100 1768773 http://peanutbutter.wordpress.com/2008/08/27/what-is-your-data-sharing-statement/ More and more funding bodies asking to make the findings of publicly funded scientific research freely available. However typically they provide limited infrastructure or recommendations as to how this should actually happen. I was wondering what type of data sharing statement researchers are (or should) be including within their grant proposals? Below is an example of how this could look. However, it provides no indication of how this could actually take place, for example via wikis, hosting on sourceforge, google code etc. It also does not imply timing, for example, this happens live, or when the grant is finished. Should the infrastructure and timing also be included? The protocols, methods and algorithms developed will be made available under the Creative Commons Attribution 3.0 Licen... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1738948 Thu, 28 Aug 2008 08:54:42 +0100 1738948 http://peanutbutter.wordpress.com/2008/08/19/is-a-knol-a-scientific-publishing-platform/ Image via CrunchBase, source unknown Google has recently released knol, which most people are calling Google’s version of Wikipedia. The main difference between a knol and a wikipedia article is that a knol has associated authorship or ownership against an article. This factor has caused some issues an outcries focusing on the merits of the wisdom of crowds verses the merits of single individuals and the whole ethos if information dissemination on the Web. (There are too many to cite but some discussion can be found on FriendFeed+knol) However, on looking at knol and having a snoop around I was not drawn into thinking about competing with Wikipedia or advertising revenue, rather what struck me is that a knol, with owner authorship looks incredibly like a scientific journal publicati... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1717077 Tue, 19 Aug 2008 17:20:10 +0100 1717077 http://peanutbutter.wordpress.com/2008/08/18/miape-gel-informatics-is-now-available-for-public-comment/ PSI logo The MIAPE: Gel Informatics module formalised by the Proteomics Standards Initiative (PSI) now available for Public Comment on the PSI Web site. Typically alot of this information will be contained in the image analysis software, so we would especially encourage software vendors to review the document. The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process. This message is to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, ... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1711717 Mon, 18 Aug 2008 08:22:07 +0100 1711717 http://peanutbutter.wordpress.com/2008/08/13/peffa-common-sequence-database-format-in-proteomics/ Image via Wikipedia PEFF:A Common Sequence Database Format in Proteomics is now available for Public Comment on the PSI Web site (http://psidev.info/index.php?q=node/363). The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process. This document presents a unified format for protein and nucleotide sequence databases to be used by sequence search engines and other associated tools (spectra library search tools, sequence alignment software, data repositories, etc). This format enables consistent extraction, display and processing of information such as protein/nucleotide sequence database entry identifier, description, taxonomy, etc. across software platforms. I... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1704632 Wed, 13 Aug 2008 13:47:53 +0100 1704632 http://peanutbutter.wordpress.com/2008/08/07/double-standards-in-nature-biotechnology/ OK, So that is a relatively inflammatory and controversial headline, edging on the side of tabloid sensationalism. What is refers to is probably a situation that I may never find myself in again, which is in this months edition of Nature Biotechnology I am an author on two, biological standards related publications. The first is a letter advertising the PSI’s MIAPE Guidelines for reporting the use of gel electrophoresis in proteomics. This letter is also accompanied by letters referring to the  MIAPE guidelines for Mass Spectrometry, Mass Spectrometry Informatics and protein modification data. The second is a paper on the Minimum Information about a Biomedical or Biological Investigations (MIBBI) registry entitled Promoting coherent minimum reporting guidelines for biological and bi... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1688925 Thu, 07 Aug 2008 20:46:08 +0100 1688925 http://peanutbutter.wordpress.com/2008/07/30/paul-meets-bill-gates/ From a heads up on a post by Jake, Paul Watson has been meeting with Microsoft and Bill Gates this week discussing cloud computing for science. Reported in a local North east media site as Microsoft leaders in thrall to Northern expertise, the report outlines cloud computing technology at Newcastle highlighting Paul’s company Inkspot science. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1668310 Wed, 30 Jul 2008 11:27:28 +0100 1668310 http://peanutbutter.wordpress.com/2008/06/25/carmen-a-scalable-science-cloud/ Paul Watson presents a talk on CARMEN a the Google Seattle Conference on Scalability. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1542979 Wed, 25 Jun 2008 10:05:26 +0100 1542979 http://peanutbutter.wordpress.com/2008/06/12/proteomics-standards-initiative-recommendations/ Several new standard artefacts have progressed through the public consultation process of the PSI. They are the MIAPE Column Chromatography document and the Mass Spectrometer Markup Language Specification (mzML). (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1512049 Thu, 12 Jun 2008 10:29:44 +0100 1512049 http://peanutbutter.wordpress.com/2008/06/12/carmen-re-branded/ We have gone through a bit of professional branding with a shiney new logo and some publicity material. The website has also been re-designed. The original drupal site was replaced with a Plone site, a decision I was not involved with. I am not sure I am a big fan of the big mug-shot which spills over the website template, the fact you have to scroll to the bottom of the front page to find out what the project is about is less than ideal. Feel free to comment (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1512050 Thu, 12 Jun 2008 10:22:58 +0100 1512050 http://peanutbutter.wordpress.com/2008/04/30/open-ed-gel-electrophoresis-data/ Several months ago - about 3, I made a public commitment to make the data I have generated during my Phd open and available online. Well I have not ignored this and in the interim I have been investigating various ways I can do this. Not only do I want to make it available but I want to structure it in a standard form, namely the gelML format. In addition, I was involved in developing it the specification and therefore, I have somewhat an obligation to use it. As it is an XML transfer format I needed to be make changes and revision it, like developing code, so in that sense recording the data on a wiki or blog would not be appropriate. For this reason I have chosen to create a google code project for gel electrophoresis data and do everything in subversion. You can browse the subversion re... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1409644 Wed, 30 Apr 2008 09:36:17 +0100 1409644 http://peanutbutter.wordpress.com/2008/04/21/how-do-you-select-you-scientific-journal/ I was trying to work out a suitable journal to where I could submit a paper on sepCV, the PSI ontology for sample preparation and separation techniques. I found my self drawing up a table, so I thought I would blog it. My initial remit is that is should be in a proteomics relevant journal as well as bioinformatics, as we are trying to encourage a greater community contribution for term collection. In this respect it has to be open access. I would also prefer the journal to accept LateX instead on proprietary formats such as word. I was really disappointed with the number of journals that only accept word documents, even PlosOne refuses anything other than word or rft, tut, tut. Based on this loose criteria, Proteome science comes top closely followed by Journal of Proteomics and Bioinforma... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1388872 Mon, 21 Apr 2008 14:24:54 +0100 1388872 http://peanutbutter.wordpress.com/2008/04/14/modeling-experiments-and-presenting-the-information/ I have struggled to keep up with this discussion, with excuses ranging from attending workshops, major release deadline on the horizon (now past) and a post-mortem on the release schedule, to attending (only to please the parents) my graduation ceremony. I am only now starting to catch up on my feeds but dauntingly Google reader tells me I have 1000+, moan moan moan, Anyway, in Cameron’s last post on the subject he points to all the previous discussions and other commentary on the topic. I will pick up from his last post and respond to some his responses to the responses to responses. I still feel that we are trying to describe and achieve different things, but that this discussion is a great way of getting to the bottom of this and achieving some clarity in our description and languag... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1370668 Mon, 14 Apr 2008 16:55:43 +0100 1370668 http://peanutbutter.wordpress.com/2008/04/07/the-first-mibbi-workshop-day-2/ The second day of the MIBBI workshop was more “free flowing” compared to the first day. During the second day we focussed on the process of MIBBI, house-keeping, infrastructure and the website. The main focus of the day was discussing what it means to be registered on the MIBBI site and be a member of the Foundry. As a straw man, rather than starting from scratch, we used the OBO foundry principles to see if they could be applied to reporting check-lists, and came up with a draft set of principles. A full “official” report of the workshop should be forthcoming. As a break from the rigorous standards development and process of reporting check-lists we went to a local restaurant and experienced anarchy when it came to understanding the menu. The meal itself was brilli... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1353863 Mon, 07 Apr 2008 15:04:16 +0100 1353863 http://peanutbutter.wordpress.com/2008/04/02/the-first-mibbi-workshop-day-1/ MIBBI is a registry of scientific experiment reporting guidelines with the idea to foster a foundry of best practice to further develop and encourage modular development and re-use of reporting guidelines. The first workshop is being held at the EBI on the 2nd - 3rd April 2008 and is a relatively closed workshop to those developers and guidelines that are registered on the site. The schedule for day one is a whistle stop tour consisting of 5 min talks (adjusting for an academics interpretation of what 5 minutes means) for all the guidelines that exist, their scope and the people behind them. Due to this I am not going to comment on individual talks. I presented two talks during the day. One on CARMEN and the development of the MINI: Electrophysiology reporting guidelines, and one, standing... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1344102 Wed, 02 Apr 2008 13:36:39 +0100 1344102 http://peanutbutter.wordpress.com/2008/03/27/a-data-model-for-life-science-experiments-fuge/ This post may be one in a series of responses to Cameron’s post on “Proposing a data model for Open Notebooks“. When I originally read this post I commented on the fact that a data model for experiments actually exists and that he may get some mileage out of it rather than starting from scratch and re-creating the wheel. Several discussions have followed on from this original post and Neil has picked up on it as well, with sentiments that I agree with. I think a large part of this discussion confuses and conflates 3 issues which I believe to be separate; the representation of experiments - the data model the presentation or level of abstraction to the user (probably some what dependent on 3.) the implementation of the data model With these three issues in mind, to start... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1331299 Thu, 27 Mar 2008 13:55:50 +0100 1331299 http://peanutbutter.wordpress.com/2008/03/26/minimum-information-about-a-neuroscience-investigation-mini/ The idea behind the CARMEN project is that we provide a system to store electrophysiology data and analysis services so that data can be shared and analysed in the “Neuro-cloud”. An important factor in realising this system is that the stored data and the services have to be described in a way that is both human and computationally amenable. The first stage of this is agreeing what information should actually be ascribed to the data. In other words, the balance between what the experimentalist want to say about their data and what informaticians need to know about a particular data set in order to perform their analysis. To this end we have defined what we believe to be the minimum information that must be ascribed to an electrophysiology experiment for submission to the CARMEN... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1327424 Wed, 26 Mar 2008 10:40:28 +0100 1327424 http://peanutbutter.wordpress.com/2008/03/13/cfp-bio-ontologies-2008-knowledge-in-biology/ Call for Papers for Bio-Ontologies 2008. Submissions are now invited Bio-Ontologies 2008: Knowledge in Biology, a SIG at Intelligent Systems for Molecular Biology 2008. Key Dates to remember: Submission due: Friday 2nd May Notifications: Friday 23rd May Final Version Due: Friday 30th May Workshop: Sunday 20th July Introduction Bio-Ontologies has existed as a SIG at ISMB for more than a decade, making it one of the longest running. For this time, Bio-Ontologies has provided a forum for discussion on the latest and most cutting edge research on ontologies. In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. Following on from last year’s reflective look, this year we are broadening the scope of SIG; we are interested i... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1301782 Thu, 13 Mar 2008 22:57:07 +0100 1301782 http://peanutbutter.wordpress.com/2008/02/22/zotero-library-re-visioned/ I have been wanting to use Zotero now for a while for my reference library but could never work out how back up my library using subversion. My life is contained within subversion, I do not know how I could have possibly survived before all my work; code, presentations, papers, images and not to mention my thesis, is all perfectly backed up and re-visioned and floating happily in the cloud available to me from any machine. Zotero installs itself inside the firefox profile which makes it difficult to revision within the C:\\my-subversion” folder. What I decided to do was to create a new firefox profile (instructions here) within my-subversion folder then install zotero creating: C:\\my-subversion\firefoxprofile\zotero I then only added the zotero folder to my subversion repository. Yo... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1250104 Fri, 22 Feb 2008 15:18:24 +0100 1250104 http://peanutbutter.wordpress.com/2008/02/18/sshh-dont-tell-anyone-about-data-sharing-for-computational-neuroscience/ I described in an earlier post that data sharing in Neuroscience is relatively non-existent. Some commentary on the subject has appeared since then via the 2007 SfN Satellite Symposium on Data Sharing entitled Value Added by Data SharingLong-TermPotentiation of Neuroscience Research, published in Neuroinformatics. I was also excited to see an article published last week Data Sharing for Computational Neuroscienc, also in Neuroinformatics. However, there is a caveat or two. Apart from ignoring all the data representation issues presented in other domains such as bioinformatics, the re-use of data models such as FuGE, or contribution to ontology efforts such as OBI, all these articles are not open access! How ironic, or should that be how embarrassing. Phil also covers this issue in his blog... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1239179 Mon, 18 Feb 2008 14:40:25 +0100 1239179 http://peanutbutter.wordpress.com/2008/01/28/standard-opened-up-science/ OK, so it is not quite up to the minute as-you-do-it-you-publish-it open science. However, I plan to make my data that I generated during my PhD (just finished) open and available, and in writing this post I am making some what of a public commitment to do so. Once difference though, from some of the open science efforts that I have seen so far, is that I will be publishing my data, conforming to the Proteomics Standards Initiative(PSI) MIAPE guidelines for gel electrophoresis (MIAPE GE.pdf) recommended reporting requirements. The data itself will be represented in XML using the PSI recommended gel electrophoresis Mark up Language (GelML), and using terminology from sepCV and OBI should mean the data set is computationally amenable. I was involved in the development of these specifications... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1182716 Mon, 28 Jan 2008 14:47:48 +0100 1182716 http://peanutbutter.wordpress.com/2008/01/07/first-wikipedia-edit/ I have just made my first edit in Wikipedia. The page in question described what now is the proliferation of life science reporting recommendations and can be found here. I added the details for the MIAPE GE recommendations and intend to add the neuroscience recommendations that I have been working on shortly. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1133770 Mon, 07 Jan 2008 10:07:29 +0100 1133770 http://peanutbutter.wordpress.com/2008/01/06/gopubmed/ In catching up with my reading lists of 2007 I was alerted to gopubmed via Deepak’s post. Gopubmed described itself as an ontology based literature search making use of both the Gene ontology and Mesh terms. There is also the ability to provide feedback or rather act as a curator for the search results. I have already noticed  some mis-match in author details.  In general though the interface  is a vast improvement on pubmed’s tiered interface and the ability to refine the searches looks interesting. I have added gopubmed to  my search engines within firefox and will have a play to see if it is any good. RSS feeds on search terms would be top of the wish list. Anybody used it in anger? (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1132110 Sun, 06 Jan 2008 21:44:43 +0100 1132110 http://peanutbutter.wordpress.com/2008/01/06/updating-blog-roll/ In an effort of catching up with the blog posts form 2007 before starting the ones for 2008, I have just gone through my Google reader subscriptions. As a result I though I would update my blogroll  accordingly with the blogs have have enjoyed reading over the last year. The list is over on the right but the new additions are bio::blogs; the monthly bioinformatics blog carnival, bioinformatics zen from Michael Barton, the CARMEN project blog (which I contribute to), Hugo Hiden, the technical director of the e-science institute here in Newcastle, Public Rambling by Pedro, Savas Parastatidis personal blog and What you’re doing is rather desperate (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1132111 Sun, 06 Jan 2008 21:18:39 +0100 1132111 http://peanutbutter.wordpress.com/2007/12/14/fuge-users-workshop/ I am at the FuGE users workshop at the moment which is being held in Manchester. The idea behind the workshop is that people who have used FuGE or extended FuGE for a specific use get together and share their experiences. I have used FuGE to develop GelML for the Proteomics Standards Initiative. GelML is one specification produced by the Gel-working group of the PSI, which is a data model to capture the use of gel electrophoresis in a proteomics experiment - but in theory it should be able to account for the use of gel electrophoresis independent of the use or domain. I presented GelML on the first day along with some discussion points I would like to see addressed over the two days. We have a small be varied set of users at the workshop covering the domains of flow cytometry, RNAi, proteo... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1094108 Fri, 14 Dec 2007 12:14:23 +0100 1094108 http://peanutbutter.wordpress.com/2007/11/14/scooped/ I have been scooped on my own work! Deepak has managed to beat me in blogging about my own screencast on the CARMEN project! Seriously though, thanks to Deepak for mentioning the project. I will have to blog harder and faster. As he highlights there are some challenges that the project hopes to address. Apart from the sheer demand for diskspace, one of the major challenges is to provide metadata to describe not only what an item of data is on the system but also how it was generated in the lab. In addition to this we also need a provenance trail describing what has been done on this data such as describing types of analysis to the degree of who authored the code, which version was it, where was it run and so on. For the lab gen... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1027033 Wed, 14 Nov 2007 15:01:24 +0100 1027033 http://peanutbutter.wordpress.com/2007/11/01/latest-bioblogs/ The 16th edition of Bio::blogs has been released on Freelancing Science. I enjoy reading Bio::blogs for two reasons: If I know it all already then I have been doing a relatively good job of keeping up to date with what has been talked about and I can convince myself that my knowledge is on the cutting edge of science ( this is rarely the case though) I always find a new blog or a new post that is interesting. This month I noticed a screencast by Konrad  on open science and transparency which I though I would download to watch on my travels to San Diego. When I got there however I realized I had already seen it via Nature Precedings. Oh well must be on the cutting edge (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=996470 Thu, 01 Nov 2007 10:33:09 +0100 996470 http://peanutbutter.wordpress.com/2007/10/31/carmen-at-sfn-demonstration-advert/ Several members of the CARMEN project, including myself, will be travelling to the Society for Neuroscience Annual Meeting next week in San Diego. We will be presenting the current status and future plans of the project on Monday 5 November from 1.30pm - 4.30pm in the Exhibition Hall at the INCF (International Neuroinformatics Coordinating Facility) Booth (4924). Come along and say hello if you are about. I hope to put the slides and the demo up as a screen cast on Bioscreencast sometime next week. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=994884 Wed, 31 Oct 2007 17:08:55 +0100 994884 http://peanutbutter.wordpress.com/2007/10/31/ontology-crowdsourcing/ I have the unenviable task of developing an ontology for the CARMEN project which will allow the process of electrophysiology experiments, the generated data, the analysis of the data and the services that perform the analysis, to be described, and in addition be computationally amenable. Collecting the words that are required to described these tasks are relatively trivial. However, getting the scientists to realise they have assigned numerous meanings to the same word or term requires a little bit more patience on my part. It also requires me to educate the scientists, in that building an ontology for electrophysiology is a little more complicated than putting some “words” in a text file. The words in an ontology have to be explicitly defined so as to be completely unambiguou... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=994885 Wed, 31 Oct 2007 13:43:20 +0100 994885 http://peanutbutter.wordpress.com/2007/10/25/e-science-blog/ A new blog has appeared over the last month entitled e-science ramblings. This blog is edited by Hugo Hiden who is the technical director of the North Eastern Regional e-Science centre which is based at Newcastle University. As described in his first post: The reason for this blog is, primarily, to document my experiences with writing a prototype e-Science research platform using Microsoft tools instead of the more traditional approach of fighting with Open Source. This way is easier, supposedly. The task I have set myself is to recreate, at a basic level, the software being developed by the CARMEN project. I think this should be an interesting read both on the technical aspects and the usability of Microsoft products compared to open source software for e-science. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=977293 Thu, 25 Oct 2007 10:25:05 +0100 977293 http://peanutbutter.wordpress.com/2007/10/18/windows-and-ubuntu-synergy/ I have just installed Synergy on my Gutsy Ubuntu machine. This allows me to switch seamlessly between my ubuntu desktop and my windows laptop using the same keyboard and mouse. It was very easy to install, via apt. I followed the ubuntu synergy how to and it worked perfectly first time. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=959702 Thu, 18 Oct 2007 10:55:27 +0100 959702 http://peanutbutter.wordpress.com/2007/09/18/how-to-install-java-on-ubuntu/ I am writing this post because I keep forgetting how to do it and end up trawling the web trying to find it. The Unbuntu starter guide should be the first port of call to install whatever flavour of java you want via apt. Then this comes from [1] If you want to use Sun’s Java instead of the open source GIJ (GNU Java bytecode interpreter) you need to set it as default. To list installed JVMs: update-java-alternatives -l To select, for example, Sun’s JVM as provided in Ubuntu 6.06, run: sudo update-java-alternatives -s java-1.5.0-sun You should also edit /etc/jvm and move /usr/lib/jvm/java-1.5.0-sun to the top of JVMs offered. To set the JAVA_HOME environment variable I followed this [2] export JAVA_HOME=/usr/lib/jvm/java-1.5.0-sun-1.5.0.08 You can find your JAVA_HOME using the l... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=880073 Tue, 18 Sep 2007 12:30:43 +0100 880073 http://peanutbutter.wordpress.com/2007/09/12/ahm-day-2/ This was a busy day on the booth for me so did not get to attend many talks. I did however attend the Keynote by Professor Tom Kirkwood entitled The Grand Challenge of Population Ageing: e-Science to the Rescue. It was a very interesting talk by a good speaker on the science behind ageing. However the e-Science to the Rescue was very thin. As this was an e-science conference I would have liked to have seen a more emphasis on the e-science. I am familiar with this project and the excellent work on an omics data portal called symba. Unfortunately symba was restricted to a slide or two that were quickly flashed up near the end of the presentation, which I found a bit of a let down. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=867200 Wed, 12 Sep 2007 17:09:00 +0100 867200 http://peanutbutter.wordpress.com/2007/09/12/all-hands-meeting-day-1/ I’m a bit late in my posting, just been to busy going to talks and discussing things, anyway. My first session at this years AHM was a workshop on “Issues is Ontology Development and Use. The welcome and workshop overview was presented by Alan Rector. I only caught the end of this introduction, as I was getting my fix of caffeine after travelling all day. The full program for the workshop and the full meeting can be found here. However there were a few presentations that stood out for me. The first one for all the wrong reasons. A talk entitled Ontology building as Practical work:Lessons from CSCW was a talk given on an overhead projector. No chance of power point poisoning tonight. Apparently he has had to step in at the last minute to give the talk so they are not his slides,... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=867201 Wed, 12 Sep 2007 14:59:55 +0100 867201 http://peanutbutter.wordpress.com/2007/09/11/conferences/ I am currently at the All Hands meeting 2007 in Nottingham, so more posts to follow with some notes on the events and presentations. In addition, a couple of people from my lab are also at the Integrative Bioinformatics conference in Ghent Belgium so you can follow Allyson’s and Matt’s comments on that event. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=861604 Tue, 11 Sep 2007 10:46:19 +0100 861604 http://peanutbutter.wordpress.com/2007/08/20/i-see-science/ It is interesting to see new developments in the dissemination of scientific discourse, such as scientific blogging and paradigms such as open science, come on-line with developments in web-based social media. The latest medium to receive the Science 2.0 treatment (poor pun on applying Web 2.0 technologies for science) is the video. YouTube is probably the granddaddy, or at least the most prominent of the video upload and broadcast services. Although YouTube doesn’t not have a defined science category, it is easy to find science related videos and lectures, mixed in with the general population. However, several specialist sites have appeared dealing specifically with science research, all have been labeled as “YouTube for science”. The most recent site is SciVee, which i... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=809505 Mon, 20 Aug 2007 13:45:20 +0100 809505 http://peanutbutter.wordpress.com/2007/08/06/scifoo/ There is lots of blogging activity at the minute around Scifoo. I am excited, just reading the posts and looking at the range of people there, not to mention the range topics on discussion. The most comprehensive one I have found is Duncan’s on Nodalpoint, and bbgm although there are other people which you can probably track via the scifoo Technorati tag I wish I was there, oh well maybe next year………. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=781252 Mon, 06 Aug 2007 10:15:10 +0100 781252 http://peanutbutter.wordpress.com/2007/07/02/rss-readers/ I have outlined my growing tendency at the minute to handing over applications to the “Internet cloud” in an earlier post. I prefer using web-based applications because I tend to jump from several machines throughout the day at work and then use a different machine at home. Having applications, floating in the ether cloud, means moving around is considerably easier. I have been using bloglines for quite a while now for my RSS feeds. I did have a early look at Google reader when it first launched, but I felt then it was not quite what I wanted and definitely not as good as bloglines at the time. However a re-visiting of Google reader over the last week or so has dramatically changed my perception. Re-vamped with a new interface (similar to bloglines) has made reading posts alot ... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=710214 Mon, 02 Jul 2007 22:14:18 +0100 710214 http://peanutbutter.wordpress.com/2007/07/02/more-on-open-science/ Thanks to everybody that commented on my post Do scientists really believe in open science? and to Open access news and Nautilus for picking up on it. It has definately stimulated some discussions James keep us posted on the outcomes of the theft of your colleagues work. This is just a note to say that Michael Barton of Bioinformatics Zen has started an open science wiki page at Nodalpoint, I think, for a special edition of Bio::blogs so feel free to comment. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=708723 Mon, 02 Jul 2007 12:55:02 +0100 708723 http://peanutbutter.wordpress.com/2007/06/26/do-scientists-really-believe-in-open-science/ I am writing this post as a collection of the current status and opinions of “Open Science”. The main reason being I have a new audience; I am working for the CARMEN e-Neuroscience project. This has exposed me, first hand, to a domain of the life-sciences to which data sharing and publicly exposing methodologies has not been readily adopted, largely it is claimed due to the size of the data in question and sensitive privacy issues. Ascoli, 2006 also endorses this view of the neuroscience and offers some further reasons why this is the case . He also includes the example of exposing neuronal morphological data and argues the benefits and counters the reticence to sharing this type of data. Hopefully, as the motivation for the CARMEN project is to store and share and facilitate t... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=696751 Tue, 26 Jun 2007 09:39:34 +0100 696751 http://peanutbutter.wordpress.com/2007/05/30/semantic-web-for-e-science/ BMC bioinformatics has released a special issue supplement on the Semantic e-science for biomedicine. It contain six papers on “the-state-of-the-art”  concerning the use of semantic web technologies in the life-sciences or biomedicine.   The topics covered range from modelling networks and pathways to,  intriguingly “traditional Chinese Medicine”. One of the papers Advancing translational medicine research with the semantic web presents an overview of the W3C Semantic Web Health Care and Life Sciences Interest Group (HCLSIG).  This paper describes the work of HCLSIG and a use-case example covering the achievements as well as the future directions of the group. Unlike many “Semantic Web” papers I have read before it presents a well grounded view of t... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=644504 Wed, 30 May 2007 08:37:58 +0100 644504 http://peanutbutter.wordpress.com/2007/03/07/no-more-session-restore-in-firefox/ I continually get greeted with the “restore last session” pop-up when I start firefox. I find it really annoying especially as I use Google Browser sync to do exactly the same thing, so I have to deal with two restore messages.  I have followed the following link and turned off the session restore feature in firefox. 1. type about:config in your browser URL 2. go to the browser.sessionstore.enabled setting 3. change the setting to false (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=485478 Wed, 07 Mar 2007 09:50:20 +0100 485478 http://peanutbutter.wordpress.com/2007/02/22/one-foot-on-the-cloud/ I am starting to realise that I am handing more and more applications over to the “cloud”. A term apparently coined by Google CEO Eric Schmid to describe web based applications and data storage. My cloud is currently composed of my email and calendar application, Bloglines ; to keep up to date with my favourite blogs, Connotea ; for my reference library, a personal wiki for general note taking, Basecamp for project management, but I mostly use the to-do list feature. My bookmarks are managed by a combination of Connotea, del.icio.us and Google browser sync and of course this blog I suppose the only thing left for day to day work would be the office tools. I have started looking at Google docs and I think it would be very useful for collaborative documents rather than 10 diffe... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=485479 Thu, 22 Feb 2007 12:29:44 +0100 485479 http://peanutbutter.wordpress.com/2007/01/12/life-science-data-standards/ The full complement of the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI), Minimum Information About a Proteomics Experiment (MIAPE), recommended reporting guidelines are now available for community review on the Nature Biotechnology website. The manuscripts range from the definition of the MIAPE concept to the individual guidelines themselves which cover, Mass Spectrometry, Mass Spectrometry Informatics, Gel Electrophoresis and Molecular Interaction experiments. A further paper on the PSI protein modification ontology (PSI-MOD) is also listed. Several other Minimum reporting requirements are also listed from other domains such as genome sequences (MIGS) and in Situ Hybridization and Immunochemistry (MISFISHIE). There is also a paper on the Functional Genomics Exp... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=485480 Fri, 12 Jan 2007 09:58:30 +0100 485480 http://peanutbutter.wordpress.com/2006/12/14/semantic-web-revolutionizing-knowledge-discovery-in-the-life-sciences/ A new book has been released on the Semantic Web and the applications in Life sciences, intuitively entitled Sematic Web: Revolutionizing Knowledge Discovery in the Life Sciences. I have purchased a similar book before entitled Ontologies for Bioinformatics and was not overly impressed with its content. This book however, as pointed out by Duncan on Nodalpoint is written by people who are actually using the technology, I have met several of the people involved in authoring some of the chapters and I think I will definitely be purchasing a copy, or rather the lab will be purchasing a copy. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=485481 Thu, 14 Dec 2006 19:42:58 +0100 485481 http://peanutbutter.wordpress.com/2006/11/23/open-data/ is a concept I came across while attending the 2nd International Digital Curation Conference and felt it deserved a post in its own right, rather than subsumed by the conference report. I am an advocate of Open Access and feel that Open Data must be a part of this process. What is the point of being able to freely read the publication if you cant freely access the data the publication refers to? The concept of Open Data was presented to me by Peter Murray-Rust, via the DCC conference, who regularly blogs about the subject. There is a Wikipedia entry which defines the concept and a mailing list which promotes discussion of Open Data. Steps are underway in the bio-science domain to define Minimum reporting requirements of data for repositories and publications. Two prominent examples are th... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=485482 Thu, 23 Nov 2006 15:01:03 +0100 485482 http://peanutbutter.wordpress.com/2006/11/23/2nd-international-digital-curation-conference/ The Data Curation Center has just held their 2nd International Digital Curation Conference, in Glasgow. The official DCC blog for the conference tracks the thoughts and discourse over the two days and the full program can be found here. As the conference name suggests, the meeting has the particular focus on different aspects of the digital curation life-cycle including managing repositories, educating data scientists and understanding the role of policy and strategy. One particular talk I was interested in was “The Roles of Shared Data Collections in Neuroscience”. This was presented by a social scientist, as the results of communications with Neuroscientists. Ironically the shared data collection was called “NeuroAnatomical Cell Repository” a pseudonym to “p... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=485483 Thu, 23 Nov 2006 14:26:48 +0100 485483 http://peanutbutter.wordpress.com/2006/11/20/carmen/ Today is my first day in my new job as a RA for the CARMEN project, which stands for Code, analysis, repository and modelling for e-Neuroscience. My role in this exciting project, is as a Metadata researcher for experiment context, which should involve ontology development and data representation in neuroscience. Just as a matter of interest I thought I would compare bioinformatics and neuroinformatics on Google Trends. Looks as if I have plenty of work to do! (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=485484 Mon, 20 Nov 2006 10:00:47 +0100 485484