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The UK e-science All Hands Meeting 2008
Posted in conference, conference report on September 9, 2008
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.
MGED by Ally
Posted in bioinformatics, conference on September 5, 2008
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.
What is your data sharing statement?
Posted in Uncategorized on August 27, 2008
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 License
- The data produced will be made available via the Science Commons, Protocol for Implementing Open Access Data.
- All source code developed will be made available under an open source license.
MIAPE: Gel Informatics is now available for Public Comment
Posted in bioinformatics, data standards, Journals Publishing, MIBBI, Proteomics on August 18, 2008
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, etc, of the proposal as a whole or of specific parts of the proposal.
If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI.
If you have comments that you would like to make but would prefer not to make public, please email the PSI editor Norman Paton.
PEFF:A Common Sequence Database Format in Proteomics
Posted in data standards, development on August 13, 2008
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. It also allows the representation of structural annotations such as post-translational modifications, mutations and other processing events. The proposed format has the form of a flat file that extends the formalism of the individual sequence entries as presented in a FASTA format and that includes a header of meta data to describe relevant information about the database(s) from which the sequence has been obtained (i.e., name, version, etc). The format is named PEFF (PSI Extended FASTA Format). Sequence database providers are encouraged to generate this format as part of their release policy or to provide appropriate converters that can be incorporated into processing tools.
This is an announcement 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, etc, of the proposal as a whole or of specific parts of the proposal.
If you do not feel well placed to comment on this document, but know someone who may be, please consider alerting them towards this information. There is no requirement that people commenting should have had any prior contact with the PSI
Double standards in Nature biotechnology
Posted in bioinformatics, data standards, Journals Publishing, MIBBI on August 7, 2008
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 biomedical investigations: the MIBBI project.
The following press release describes this paper in more detail.
More than 20 grass-roots standardisation groups, led by scientists at the European Bioinformatics Institute (EMBL-EBI) and the Centre for Ecology & Hydrology (CEH), have combined forces to form the “Minimum Information about a Biomedical or Biological Investigation” (MIBBI) initiative. Their aim is to harmonise standards for high-throughput biology, and their methodology is described in a Commentary article, published today in the journal Nature Biotechnology.
Data standards are increasingly vital to scientific progress, as groups from around the world look to share their data and mine it more effectively. But the proliferation of projects to build “Minimum Information” checklists that describe experimental procedures was beginning to create problems. “There was no way of even finding all the current checklist projects without days of googling,” says the EMBL-EBI’s Chris Taylor, who shares first authorship of the paper with Dawn Field (CEH) and Susanna-Assunta Sansone (EMBL-EBI). “As a result, much of the great work that’s going into developing community standards was being overlooked, and different communities were at risk of developing mutually incompatible standards. MIBBI will help to prevent them from reinventing the wheel.
The MIBBI Portal already offers a one-stop shop for researchers, funders, journals and reviewers searching for a comprehensive list of minimum information checklists. The next step will be to build the MIBBI Foundry, which will bring together diverse communities to rationalise and streamline standardisation efforts. “Communities working together through MIBBI will produce non-overlapping minimal information modules,” says CEH’s Dawn Field. “The idea is that each checklist will fit neatly into a jigsaw, with each community being able to take the pieces that are relevant to them.” Some, such as checklists describing the nature of a biological sample used for an experiment, will be relevant to many communities, whereas others, such as standards for describing a flow cytometry experiment, may be developed and used by a subset of communities.
“MIBBI represents the first new effort taking the Open Biomedical Ontologies (OBO) as its role model”, says Susanna-Assunta Sansone. “The MIBBI Portal operates in a manner analogous to OBO as an open information resource, while the MIBBI Foundry fosters collaborative development and integration of checklists into self-contained modules just like the OBO Foundry does for the ontologies”.
There is a growing understanding of the value of such minimal information standards among biologists and an increased willingness to work together across disciplinary boundaries. The benefits include making experimental data more reproducible and allowing more powerful analyses over diverse sets of data. New checklist communities are encouraged to register with MIBBI and consider joining the MIBBI Foundry.
Press release issued by the EMBL-European Bioinformatics Institute and the Centre for Ecology and Hydrology, UK.
Paul meets Bill Gates
Posted in cloud on July 30, 2008
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.
CARMEN – A Scalable Science cloud
Posted in bioinformatics, CARMEN, cloud, conference, data standards, neuroinformatics, open science, video on June 25, 2008
Paul Watson presents a talk on CARMEN a the Google Seattle Conference on Scalability.
Proteomics Standards Initiative recommendations
Posted in bioinformatics, data standards, development, Proteomics, Uncategorized on June 12, 2008
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).