Archive for category Proteomics

MIAPE: Gel Informatics is now available for Public Comment

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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.

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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).

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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 repository or check it out anonymously. The geML file that will eventually (as its still very much a work in progress) contain the data is here. As I am doing this, I though I might as well publish my lab book while I was at it. This will be done using LateX and the pdf that gets generated can be found here.

To date, this is still a work in progress and a reverse engineering project, as the experiments are not being done live. It may take a while to complete but in the end I hope presenting my data in gelML and making my labbook available can be more of a benefit than decomposing for years on cellulose.

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How do you select your 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 Bioinformatics (if I sacrifice using word for open access). BMC Bioinformatics also ticks all the boxes but it misses out on the proteomics audience. The table below also includes Impact factor, but I did not really take that into consideration. Wouldn’t it be nice is there was an app that you could just enter in criteria like this, target audience, submission format, copyright, etc and get back the journals that meet these requirements. Something like this would save me an afternoon trawling through the web building spreadsheets.

How do you select your journal?

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Journal Word Latex Open Access Impact Factor

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Proteomics Yes NO cant find statement 5.735

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Journal of Proteomics and Bioinformatics Yes NO Yes

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Biomedical Informatics Yes Yes NO 2.346

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BMC Bioinformatics Yes Yes Yes 3.62

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PlosONE Yes No Yes

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Proteome Science Yes Yes Yes

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Proteomics research Yes Yes No 5.151

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Standard Open(ed-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 so I suppose I should be leading by example and be the first one to publish a complete gel electrophoresis proteomics dataset.

When finnished, I would have liked it to be published some where like Nature Preceedings, however they only accept proprietary Microsoft files and pdfs rather than XML documents. I also though of creating a Google code project for it, but it seems quite elaborate for something nobody else would be contributing to and once completed would be rather static. Any suggestions are very welcome.

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My Lab work has finnished!

lastgel.gif

Hurray! At last I have ran my final 2D gel for my PhD, no more crying over spilt acrylamide. Only joking I have never spilt acrylamide :). Now I have three months left to do nothing but bioinformatics and of course the dreaded write up. Maybe a could design an ontology that could infer my thesis from all the data I give it. Any way I though I would post a picture of my last gel so you can all marvel at a bioinformatician who can run 2D gels.

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