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Experimental Officer in Bioinformatics and Metabolomics
Fixed-term for 3 years in the first instance

As part of a £8 million award from the MRC, industry and University of Birmingham, we have established a state-of-the-art metabolic phenotyping (metabolomics) facility to conduct medical research including the development of stratified medicine approaches. Phenome Centre Birmingham (PCB), which was formally opened on 23 May 2016 by the UK Government's Chief Scientific Advisor Sir Mark Walport ( http://www.birmingham.ac.uk/news/latest/2016/05/Phenome-Centre-Birmingham.aspx ), is applying eleven new liquid chromatography-mass spectrometers (LC-MS), two new Bruker 600 MHz NMR spectrometers, liquid handling robots and high specification computational infrastructure to better understand metabolic perturbations in human health, disease and ageing. The facility is anticipated to conduct tens of thousands of analyses of human samples per year, creating genuinely "Big Data", with extensive clinical metadata. It is based alongside one of the largest hospitals in Europe, the Queen Elizabeth Hospital at Birmingham, and the new £24 million Institute of Translational Medicine. In addition, the PCB will interact closely with the MRC-NIHR National Phenome Centre in London and the new international network of Phenome Centres to enhance metabolic phenotyping in the UK and globally.

We seek a highly motivated bioinformatician to join the 10-person PC-B team and contribute to fulfilling the research objectives of this centre with a focus on developing, implementing and applying bio- and chemo-informatics tools for the integration and analysis of clinical metadata and metabolic phenotyping data (i.e. mass spectrometry and/or NMR); tools for metabolite identification; and/or statistical bioinformatics. This will include implementing automated data processing pipelines, contributing to experimental design, undertaking statistical and computational analyses, and interpretation of large scale metabolomics datasets. Further opportunities include collaborating with clinical scientists and contributing to training courses in the Birmingham Metabolomics Training Centre ( http://www.birmingham.ac.uk/bmtc ).

Applicants should hold a PhD (awarded) in computational metabolomics, chemoinformatics, bioinformatics, biostatistics or a closely related area, with experience and demonstrated success of working independently and as part of a large team in a bioanalytical or academic research facility in industry or academia as well as having a growing national reputation in metabolomics and/or bioinformatics/biostatistics.

The University offers a variety of courses for personal development of its employees. The University of Birmingham is a family-friendly employer. The School of Biosciences welcomes flexible and part-time working to suit family or other commitments. The University has on-campus childcare facilities.

The post is available in the first instance for 3 years with the expectation for significant extension subject to the success of Phenome Centre Birmingham. Informal enquiries can be addressed to Professor Mark Viant (tel: +44 (0)121 414 2219 or email: M.Viant@bham.ac.uk) or Dr Warwick Dunn (tel: +44 (0)121 414 5458 or email: W.Dunn@bham.ac.uk).

For further information or to apply visit: https://atsv7.wcn.co.uk/search_engine/jobs.cgi?SID=amNvZGU9MTYyMTI1MSZ2dF90ZW1wbGF0ZT03Njcmb3duZXI9NTAzMjUyMSZvd25lcnR5cGU9ZmFpciZicmFuZF9pZD0wJnZhY2Zpcm0udmFjdGl0bGU9NTUxOTImcG9zdGluZ19jb2RlPTExNw==
Closing date: 26th April 2017
Reference Number: 55192

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Update: we managed to reinstall Thermo Foundation from version 3. That seems to have solved it! :-) No more dll errors.
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I know someone who had the same experience and they were advised that Windows 10 has not been tested thoroughly for Xcalibur, so it's not supported yet. That person went back to Windows 7 for the time being.

If anyone has a solution, please post! :-)
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Hi,

Does anybody has experience trying to install Xcalibur software on a Windows 10 machine?
I run into DLL issues - the program wouldn't open or get deleted from the laptop without 'forceful' handling.
Are there any patches around to fix this?
It was the newest version 4.0.27 that I am trying to run....

Thanks for advice,

Justin


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Announcements / Re: Metabolomics Society conference 2017
Last post by Dara Daygon -
Hello, we're the local organising committee of the conference in Brisbane! Please follow our facebook page https://www.facebook.com/Metabolomics2017 and tweet with the hashtag #metabolomics2017 for the most recent news about the conference.
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XCMS / Re: Inconsistent integration borders in EICs
Last post by NShore -
More specifically, I've tried to use the retexp function to manually fix integration borders on the extracted @peaks. This works for the EICs, as shown in the two plots attached, however, the into values and rtmin/rtmax in the diffreport are unaffected. How would I make this work on actual integration values?

Also, especially rtmin/rtmax in the diffreport don't seem to correspond with anything, really, as they usually only differ by a few seconds, when they should be in the order of magnitude of 50-100 seconds for most peaks.  I'm assuming here that these simply show the spread of rtmed values within the group?
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XCMS / Re: Inconsistent integration borders in EICs
Last post by NShore -
When I look into the peak list for my xcmxSet prior to diffreport generation (but I assume at all stages), I do find varying peak widths for one mass/RT combination, as in, RT will be the same, but RTmin and RTmax will differ.

Would there be a way to manually set the integration borders either to a fixed length, or to either the minimum or maximum of each peak in every group? As in, fix RTmin and RTmax prior to integration, per peak group?
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What happens if you split the file into two mass ranges using MSconvert? Using the subset filter.
Also I seem to remember that the Qex sometimes does something strange with the data file: it will label one scan as "full scan" and the other as "SIM". You can check that when going through the scans in Xcalibur. If that's the problem, there is a way to get your data into mz(X)ML correctly, I would have to look it up though.
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What are your MSconvert settings? Make sure to use peakPicking with "prefer vendor" activated.
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This is the correct link https://www.ebi.ac.uk/training/events/2017/metabolomics-workflows
Topics: 
  • OpenMS workflows
  • Knime workflows
  • PhenoMeNal/ MetaboLights