http://wiki.proteomics-academy.org/mediawiki/api.php?action=feedcontributions&user=Jg&feedformat=atomEuropean Proteomics Academy - User contributions [en]2024-03-29T13:20:29ZUser contributionsMediaWiki 1.32.0http://wiki.proteomics-academy.org/mediawiki/index.php?title=Project:EuBICGuidelines&diff=527Project:EuBICGuidelines2019-10-11T11:59:48Z<p>Jg: EuBIC Guidelines Project</p>
<hr />
<div>This project tries to define guidelines that ensure that a (MS-based) publication contains all information required to ensure that the reported data reproducible.<br />
<br />
== Guidelines ==<br />
<br />
https://eubic.github.io/ReproducibleMSGuidelines shows a nicely rendered version of the current guidelines.<br />
<br />
The guidelines are recorded in the GitHub repository: https://github.com/EuBIC/ReproducibleMSGuidelines<br />
<br />
All changes to the guidelines should only be made there.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Projects&diff=526Projects2019-10-11T11:46:10Z<p>Jg: Added guidelines project</p>
<hr />
<div>This page gives an overview over all projects currently supported or coordinated by EuBIC.<br />
<br />
All new project pages should be in the '''Project:''' namespace (ie. "Project:TheGreatProject").<br />
<br />
== Community ==<br />
<br />
'''[[Project:EuBICGuidelines| EuBIC Guidelines for MS Experiments]]:'''<br />
<br />
Develop guidelines that describe the minimal information required to ensure that an MS-based publication is reproducible.<br />
<br />
'''[[Project:JobFair| Job Fair]]:''' <br />
<br />
This project is run in collaboration with the YPIC initiative to create a job portal for proteomics / bioinformatics associated jobs. Further plans exist to implement a "talent pool" where researchers looking for a new job can provide e.g. their CVs.<br />
<br />
'''[[Project:FindABioinformatician| Find A Bioinformatician]]:'''<br />
<br />
This project is intended to create a platform for research groups to post a research question / dataset to find a collaboration with a bioinformatician to analyse the data.<br />
<br />
'''[[Project:QC| Quality Control]]:'''<br />
<br />
EuBIC collaborates with the Quality Control working group of the HUPO-PSI to develop novel standards and tools for biological mass spectrometry.<br />
<br />
'''[[Project:ASMS2017|EuBIC activities at ASMS 2017]]'''<br />
<br />
'''[[Project:HUPO2017| EuBIC activities at HUPO 2017]]'''<br />
<br />
'''[[Project:EUPA2018| EuBIC activities at EUPA 2018]]'''<br />
<br />
Developer meeting 2018<br />
<br />
EuBIC winter school 2019</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Educational_Videos&diff=387Educational Videos2018-10-09T15:38:05Z<p>Jg: Added link to new Sequest talk by John Yates</p>
<hr />
<div>You will find in this section a selection of videos on proteomics as well as recordings of scientific lectures that should assist anyone interested in proteomics to learn more about the field.<br />
<br />
<br />
== Outreach ==<br />
<br />
{| class="wikitable"<br />
! Title !!Audience !!Description<br />
|-<br />
|[[Video:Proteins at work|Proteins at work - the fascinating world of proteomics]] || All || Introduction to the fascinating world of proteomics by the [http://www.hecklab.com Heck lab]<br />
|-<br />
|[[Video:What is Proteomics|What is Proteomics]] || All || What is proteomics? by the [http://www.childrenshospital.org/research-and-innovation/research/labs/steen-laboratory Steen & Steen Laboratory]<br />
|}<br />
<br />
== Scientific Lectures ==<br />
<br />
{| class="wikitable"<br />
! Title !!Audience !!Description<br />
|-<br />
|[https://www.youtube.com/watch?v=KCTjL6KmfGg&feature=youtu.be The Invention of Sequest]<br />
|Beginner / Intermediate<br />
|Lecture by John Yates on the invention of Sequest @ SCP2018<br />
|-<br />
|[[Videos:BroadE 2012 Proteomics Workshop|BroadE 2012 Proteomics Workshop]] || Beginner / Intermediate || Lectures held at the BroadE 2012 Proteomics Workshop<br />
|-<br />
|[[Videos:9th European Summer School|9th European Summer School]] || Beginner / Intermediate || These are all lectures held at the 9th European Summer School in 2015<br />
|}<br />
<br />
== Online Video Tutorials ==<br />
<br />
{| class="wikitable"<br />
! Title !!Category !!Description<br />
|-<br />
|[[Video-Tutorial:Pladipus|Pladipus]] || Intermediate / Advanced || Video tutorial on how to set a distributed computing system using [https://compomics.github.io/projects/pladipus.html Pladipus] by Kenneth Verheggen.<br />
|-<br />
|[https://vimeo.com/97952461 Cross Linking] || Intermediate / Advanced || Video tutorial on how to idenify cross linked peptides using [http://prospector.ucsf.edu/prospector/mshome.htm ProteinProspector] by Robert Chalkley.<br />
|}</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Main_Page&diff=359Main Page2018-02-08T20:58:18Z<p>Jg: Added FB link to YPIC paragraph</p>
<hr />
<div>= Proteomics Academy by EuBIC and EuPA =<br />
[[File:Eupa_logo.png|159x159px|right|link=http://www.eupa.org]]<br />
<br />
[[File:Eubic_logo.png|149x149px|link=http://www.proteomics-academy.org]]<br />
<br />
The Proteomics Academy is an education platform created by the the [http://www.eupa.org/ European Proteomics Association (EuPA)] educational committee and the [http://www.proteomics-academy.org European Bioinformatics Community (EuBIC)] initiative to foster exchange of knowledge on proteomics. We organize training events throughout Europe and provide as many of the used training materials on this website.<br />
<br />
People involved in the European Proteomics Academy including scientific advisory board and the education committee can be found [[European Proteomics Academy:People|here]].<br />
<br />
<br />
== Courses ==<br />
<br />
The [http://eupa.org EuPA] organizes proteomics courses through Europe.<br />
<br />
The [[EuPA:Courses]] section provides a complete list of courses.<br />
<br />
<br />
== Tutorials ==<br />
<br />
You will find in this section a selection of online free tutorials to learn more about proteomics.<br />
<br />
The [[Tutorials]] section provides the entry point to all tutorials found on this site.<br />
<br />
<br />
== Educational Videos ==<br />
<br />
You will find in this section a selection of online videos to learn more about proteomics.<br />
<br />
The [[Educational Videos]] section provides the entry point to all educational videos found on this site.<br />
<br />
== Protocols ==<br />
<br />
You will find in this section a selection of protocols to prime your experiments.<br />
<br />
The [[Protocols]] section provides the entry point to all protocols found on this site.<br />
<br />
== Young Proteomics Investigator Club (YPIC) ==<br />
YPIC is a<br />
sister organization of EuBIC. We support all young proteomics researchers in<br />
their career development. We want<br />
to represent all the extra-scientific aspects of being a young scientist.<br />
<br />
You can find a glimpse of<br />
our activities on [https://www.facebook.com/EuYPIC facebook.com/EuYPIC]. You are more than welcome to become a<br />
free member here and think along with us by filling out our survey. <br />
<br />
And we have a challenge<br />
too: a protein encoding an English sentenced, expressed in E. coli! </div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=MediaWiki:Sidebar&diff=356MediaWiki:Sidebar2017-09-20T10:00:44Z<p>Jg: </p>
<hr />
<div><br />
* navigation<br />
** mainpage|Proteomics Academy<br />
* Education<br />
** Courses|Courses<br />
** Tutorials|Tutorials<br />
** Educational Videos|Educational Videos<br />
** Protocols|Protocols<br />
* Service<br />
** http://jobs.proteomics-academy.org|Jobs<br />
** Grants|Grants<br />
* EuBIC<br />
** Projects|Ongoing Projects<br />
* External Links<br />
** http://www.proteomics-academy.org/|Proteomics Academy<br />
** http://www.eupa.org|EuPA<br />
* Site Information<br />
** recentchanges-url|recentchanges<br />
** helppage|help<br />
* SEARCH<br />
* TOOLBOX<br />
* LANGUAGES</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Projects&diff=354Projects2017-09-20T09:30:00Z<p>Jg: Added link to Submission Review project</p>
<hr />
<div>This page gives an overview over all projects currently supported or coordinated by EuBIC.<br />
<br />
All new project pages should be in the '''Project:''' namespace (ie. "Project:TheGreatProject").<br />
<br />
== Community ==<br />
<br />
'''[[Project:JobFair| Job Fair]]:''' <br />
<br />
This project is run in collaboration with the YPIC initiative to create a job portal for proteomics / bioinformatics associated jobs. Further plans exist to implement a "talent pool" where researchers looking for a new job can provide e.g. their CVs.<br />
<br />
'''[[Project:FindABioinformatician| Find A Bioinformatician]]:'''<br />
<br />
This project is intended to create a platform for research groups to post a research question / dataset to find a collaboration with a bioinformatician to analyse the data.<br />
<br />
'''[[Project:QC| Quality Control]]:'''<br />
<br />
EuBIC collaborates with the Quality Control working group of the HUPO-PSI to develop novel standards and tools for biological mass spectrometry.<br />
<br />
'''[[Project:SubmissionReview| Submission Review]]:'''<br />
<br />
This project focuses on the idea to create a report format on data deposition for paper review.<br />
<br />
'''[[Project:ASMS2017|EuBIC activities at ASMS 2017]]'''<br />
<br />
'''[[Project:HUPO2017| EuBIC activities at HUPO 2017]]'''<br />
<br />
'''[[Project:EUPA2018| EuBIC activities at EUPA 2018]]'''<br />
<br />
Developer meeting 2018<br />
<br />
EuBIC winter school 2019</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Project:JobFair&diff=351Project:JobFair2017-09-19T15:54:19Z<p>Jg: Updated to say that jobsite is done</p>
<hr />
<div>The '''Job Fair''' project is run in collaboration with the EuYPIC initiative to create a job portal for proteomics / bioinformatics jobs.<br />
<br />
== Resources ==<br />
<br />
The job fair was now officially launched at HUPO 2017 and is available at http://jobs.proteomics-academy.org<br />
<br />
As a main feature it supports the posting of CVs. Thereby, anyone coming to the end of his or her contract can already advertise on this platform.<br />
<br />
== People ==<br />
<br />
* [[User:jg|Johannes Griss]]</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=MediaWiki:Sidebar&diff=349MediaWiki:Sidebar2017-07-09T17:57:55Z<p>Jg: Adapted jobs link</p>
<hr />
<div><br />
* navigation<br />
** mainpage|Proteomics Academy<br />
* Education<br />
** Courses|Courses<br />
** Tutorials|Tutorials<br />
** Educational Videos|Educational Videos<br />
** Protocols|Protocols<br />
* Service<br />
** http://jobs.proteomics-academy.org|Jobs<br />
** Grants|Grants<br />
* External Links<br />
** http://www.proteomics-academy.org/|Proteomics Academy<br />
** http://www.eupa.org|EuPA<br />
* Site Information<br />
** recentchanges-url|recentchanges<br />
** helppage|help<br />
* SEARCH<br />
* TOOLBOX<br />
* LANGUAGES</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Jobs&diff=348Jobs2017-07-09T17:56:31Z<p>Jg: Deprecated jobs site.</p>
<hr />
<div>__FORCETOC__<br />
<br />
'''DEPRECATED'''<br />
<br />
This page is no longer in use. Our new job portal can be found at http://jobs.proteomics-academy.org.<br />
<br />
<br />
<br />
This page is a collection of job advertisements focused on people with bioinformatics expertise. To post a job, simply edit this page, see instructions [[Jobs|below]].<br />
<br />
== Academia ==<br />
<br />
{| class="wikitable sortable"<br />
|-<br />
! Position <br />
!Category!! Country !! City !! Institute !! Description !! Expiring date<br />
! Contact !! Link <br />
|-<br />
|-<br />
|-<br />
|-<br />
|PhD<br />
|Data Visualization<br />
|Norway<br />
|Bergen<br />
|University of Bergen<br />
|At the Department of Informatics there are up to two PhD positions in the field of visualization available, within the project “MetaVis”, financed by the Research Council of Norway and the University of Bergen. The position is for a fixed-term period of 4 years.<br />
|2017-06-18<br />
|stefan.bruckner@uib.no<br />
|[https://www.jobbnorge.no/en/available-jobs/job/138313/phd-position-in-visualization-up-to-two-positions job offer]<br />
|-<br />
|Data Analyst<br />
|Bioinformatics/Computational Biology<br />
|Austria<br />
|Vienna<br />
|Max F. Perutz Laboratories<br />
|The Baccarini lab seeks to recruit a Data Analyst who will systematically analyze and integrate large-scale data sets, including (epi)genomics data and mass spectrometry results, originating from our ongoing projects in molecular and cell biology. The successful candidate will develop an optimized data structure, build systematic analysis pipelines, and analyze the data by placing them in context with existing datasets.<br />
'''Working environment''': The Baccarini lab focuses on the role of protein complexes in the signaling pathways that integrate basic biological processes such as proliferation, differentiation, and migration. Projects focus on the analysis of such complexes and their impact on gene expression and the determination of cell fate. The lab is part of the PhD program “Signaling Mechanisms In Cellular Homeostasis”, which comprises a total of 14 groups working on different molecular aspects of cellular/organismal adaptation. The groups use CRISPR-Cas9 or RNAi screens, mass spectrometry and NGS to address their research questions. The selected candidate will work in an innovative research environment and collaborate closely with other groups at the Max F. Perutz Laboratories.<br />
<br />
'''Requirements''': Applicants must hold a Master or PhD degree in Computational Biology and ideally have a proven track record in data integration, analysis and statistics. Expertise in programs such as R, Python, Matlab as well as excellent written and oral communication skills in English, high accuracy, reliability and interpersonal and organizational skills are a requirement.<br />
<br />
'''Application''': Interested candidates should send their application documents including a cover letter, a CV/publication list, and the names of three referees.<br />
|2017-05-21<br />
|manuela.baccarini@univie.ac.at<br />
|<br />
|-<br />
|PostDoc<br />
|Proteomics / Computational Biology<br />
|Austria<br />
|Salzburg<br />
|Univ. of Salzburg<br />
|A postdoctoral researcher position is available in theChristian Doppler Laboratory for Biosimilar Characterization at the University of Salzburg. The laboratory is a collaboration of five academic research groups and two industrial partners with a focus on therapeutic protein characterization. The candidate will set up experimental plans to systematically organize workflows, data collection and data storage, and interact with programmers of industrial collaborators to install and implement new software components, program suitable scripts and algorithms aiding data conversion and interpretation according to regulations of Good Manufacturing Practice.<br />
|2020-09<br />
|c.huber@sbg.ac.at<br />
|[https://euraxess.ec.europa.eu/jobs/165196 job offer]<br />
|-<br />
|PhD / staff scientist<br />
|Bioinformatics / Proteomics<br />
|Germany<br />
|Bochum<br />
|Ruhr-Universität Bochum<br />
|The Medical Bioinformatics group of the Medizinisches Proteom-Center is looking for a bioinformatician, to adapt / improve scientific analysis software for cloud computing. For more information about the position, please see the posted link.<br />
|2018-02<br />
|martin.eisenacher@rub.de<br />
|[https://www.stellenwerk-bochum.de/jobboerse/wissenschaftl-mitarbeiterin-bio-informatikerin-bio-informatiker-bo-2017-02-17-104803 job offer]<br />
|-<br />
|PhD / staff scientist<br />
|Statistics<br />
|Germany<br />
|Bochum<br />
|Ruhr-Universität Bochum<br />
|The Medical Bioinformatics group of the Medizinisches Proteom-Center is looking for a statistician for the analysis of quantitative proteomics data. This includes the planning of the experiment and an adequate analysis method. For more information about the position, please see the posted link.<br />
|2018-12<br />
|martin.eisenacher@rub.de<br />
|[https://www.stellenwerk-bochum.de/jobboerse/wissenschaftl-mitarbeiterin-statistikerin-statistiker-bo-2017-02-22-105438 job offer]<br />
|-<br />
|}<br />
<br />
== Industry ==<br />
<br />
{| class="wikitable"<br />
!Position<br />
!Category<br />
!Country<br />
!City<br />
!Institute<br />
!Description<br />
!Expiring date<br />
!Contact<br />
!Link<br />
|-<br />
|Remote Part-Time Bioinformatician<br />
|Proteomics Bioinformatics<br />
|Anywhere<br />
|Anywhere<br />
|DeepDIA<br />
|We are seeking a bioinformaticist for a few hours/week (as much as you are interested in devoting) to work from anywhere (with a decent internet connection) to help design, implement, and test truly sophisticated informatics algorithms for DIA informatics on Thermo Fusion/Lumos/QE and Sciex 5600/6600 instruments. The algorithms are absolutely state-of-the-art, and they are also running on state-of-the-art massively parallel computation infrastructure (think 100s of CPU cores), so it sometimes requires "a different way of thinking". We are currently 3 bioinformaticists plus 6 software engineers, all working from around the world. The work is exciting, paid, and can be part of your publication material or even current academic research (some aspects may be more confidential than others, but they are few and should not prevent publication.) The intention is that our work will be used by big pharma, government, and academia, and we already have ~6 different organizations collaborating with us presently that fall into those 3 categories.<br />
<br />
'''Skills sought:''' strong CS background (either from school & or from years of experience); strong knowledge of proteomics informatics (ie you could rewrite a search engine as sophisticated as MaxQuant if you really had to etc.); Java; Linux etc.<br />
<br />
'''Hours worked:''' A few of your hours worked should overlap with normal US East Coast business hours so that we can do team google hangouts easily etc.<br />
|2017-03-31<br />
|gautam.saxena@deepdia.com<br />
|<none yet><br />
|-<br />
|Staff scientist<br />
|Computational Biology / Oncology<br />
|Germany<br />
|Cologne<br />
|NEO New Oncology GmbH<br />
|NEO New Oncology GmbH – part of Siemens Healthineers – is a dynamically growing diagnostics company offering genetic testing to identify optimal treatment options for cancer patients. Our technology platform “NEO” is based on next generation sequencing and proprietary computer algorithms. NEO reliably identifies therapy-relevant genetic alterations from standard clinical material such as FFPE specimens and liquid biopsies with short turnaround times and highest accuracy.<br />
The Computational Biology department is seeking a highly motivated '''Computational Biologist (m/f)''' with strong track record in the field of bioinformatics and/or computational biology to strengthen the existing team of outstanding international scientists and computational biologists contributing to the improvement of the New Oncology cutting-edge technology.<br />
|<br />
|jobs@newoncology.de<br />
|[http://www.jobvector.de/jobs-stellenangebote/healthcare-gesundheitswesen/klinische-forschung/computational-biologist-m-f-85967.html job offer]<br />
|-<br />
|Staff scientist<br />
|Computational Biology / Bioinformatics / Oncology<br />
|Germany<br />
|Cologne<br />
|NEO New Oncology GmbH<br />
|NEO New Oncology GmbH – part of Siemens Healthineers – is a dynamically growing diagnostics company offering genetic testing to identify optimal treatment options for cancer patients. Our technology platform “NEO” is based on next generation sequencing and proprietary computer algorithms. NEO reliably identifies therapy-relevant genetic alterations from standard clinical material such as FFPE specimens and liquid biopsies with short turnaround times and highest accuracy.<br />
The Computational Biology department is seeking a highly motivated '''Computational Biologist / Bioinformatician (m/f)''' with strong track record in the field of bioinformatics and/or computational biology to strengthen the existing team of outstanding international scientists and computational biologists contributing to the improvement of the New Oncology cutting-edge technology.<br />
|<br />
|jobs@newoncology.de<br />
|[http://www.jobvector.de/jobs-stellenangebote/healthcare-gesundheitswesen/klinische-forschung/computational-biologist-bioinformatician-m-f-85965.html job offer]<br />
|}<br />
<br />
== How to post a job ==<br />
<br />
If you are interested in posting a job, simply register for this wiki and edit this page.<br />
<br />
The fields in the table should be filled out according to these guidelines:<br />
* '''Position''': PhD, PostDoc, Staff scientist, Group leader<br />
* '''Category''': Use key words to help applicants see the field of application.<br />
* '''Country''': Name of the country written out, ''e.g.'' Austria.<br />
* '''Institute''': The institute's name.<br />
* '''Description''': A very short description about the main requirements for this job and the main duties. This should not be a detailed job description but only a short summary.<br />
* '''Epiring date''': The expiring date in the format YYYY-MM-DD. Expired announcements are moved to the [[Jobs|Archive]] section.<br />
* '''Contact''': Primary means of contact for this job offer.<br />
* '''Link''': Link to the official job posting at your institute's website.<br />
== Archive ==<br />
This section lists expired job offers.<br />
* '''Academia'''<br />
{| class="wikitable sortable"<br />
|-<br />
! Position <br />
!Category!! Country !! City !! Institute !! Description !! Expiring date<br />
! Contact !! Link <br />
|-<br />
|PostDoc<br />
|Bioinformatics / Computational Biology<br />
|Germany<br />
|Hohenheim<br />
|University of Hohenheim<br />
|Currently, the CFH consists of three modules: Analytical Chemistry, Mass Spectrometry, and Spectroscopy, providing high-throughput technologies particularly in the areas of Proteomics (MS), Metabolomics (MS/NMR) and Ionomics (ICP-MS, ICP-AES).<br />
In the frame of a DFG-funded project, the newly created unit “Data Management and Bioinformatics” aims to facilitate and drive the exploration of connections and correlations between data obtained by different analytical techniques. In particular, the goals are to implement a common data storage and exchange system for the currently existing CFH modules, to find means for integrated data analysis of multi-omics datasets and to support and train CFH users in experimental design and (statistical) data analysis.<br />
|2017-04-15<br />
|cfh@unihohenheim.de<br />
|[http://www.jobvector.de/jobs-stellenangebote/informatik/datenbanken-datenverarbeitung/bio-informatician-computational-biologist-computer-scientist-data-management-and-bioinformatics-m-f-85368.html job offer]<br />
|-<br />
|Staff Scientist<br />
|Bioinformatics / Computational Biology<br />
|Germany<br />
|Hohenheim<br />
|University of Hohenheim<br />
|Currently, the CFH consists of three modules: Analytical Chemistry, Mass Spectrometry, and Spectroscopy, providing high-throughput technologies particularly in the areas of Proteomics (MS), Metabolomics (MS/NMR) and Ionomics (ICP-MS, ICP-AES).<br />
In the frame of a DFG-funded project, the newly created unit “Data Management and Bioinformatics” aims to facilitate and drive the exploration of connections and correlations between data obtained by different analytical techniques. In particular, the goals are to implement a common data storage and exchange system for the currently existing CFH modules, to find means for integrated data analysis of multi-omics datasets and to support and train CFH users in experimental design and (statistical) data analysis.<br />
|2017-04-15<br />
|cfh@unihohenheim.de<br />
|[http://www.jobvector.de/jobs-stellenangebote/informatik/datenbanken-datenverarbeitung/bio-informatician-computational-biologist-computer-scientist-data-management-and-bioinformatics-m-f-85368.html job offer]<br />
|-<br />
|PostDoc<br />
|Proteomics Bioinformatics<br />
|Australia<br />
|Melbourne<br />
|Monash University<br />
|We are seeking a highly motivated and talented postdoctoral scientist to join our research groups. Your main responsibility will be to independently assist collaborators and clients of the Monash Biomedical Proteomics Facility and the Monash Bioinformatics Platform by conducting in-depth analyses of proteomics data.<br />
<br />
You should hold a PhD preferably in Bioinformatics or in a relevant field. Knowledge and experience in proteomics and/or proteomics data analysis will be highly regarded.<br />
<br />
Candidates with a promising track record in the relevant areas and a proven publication record in international journals are encouraged to apply.<br />
<br />
This role is a full-time position; however, flexible working arrangements may be negotiated.<br />
|2017-04-17<br />
|Associate Professor David Powell, Director, Monash Bioinformatics Platform, School of Biomedical Sciences, +61 3 9902 9150<br />
|[https://www.seek.com.au/Job/33137193 job offer]<br />
|-<br />
|PostDoc<br />
|Spectroscopy / Chemometrics<br />
|Austria/ Switzerland<br />
|Vienna/ Zurich<br />
|Vetmed Vienna/ Uni Zurich<br />
|Successful translation and implementation of a tool for the differentiation of fresh from previously frozen meat based on chemometric-assisted FTIR spectroscopy from laboratory scale to a working prototype in the field.<br />
We are looking for an applicant holding a PhD in chemometrics, bioinformatics or equivalent, with advanced skills in multivariate statistical analyses and modeling, including AI systems, such as neural networks, support vector machines etc. A background or interest in spectroscopy (FTIR, NIR, Raman, UV/Vis), as well as project management and advanced communication and writing skills in English are required.<br />
|2017-05-01<br />
|sophia.johler@uzh.ch/ tom.grunert@vetmeduni.ac.at<br />
|<br />
|-<br />
|Staff scientist<br />
|Bioinformatics / Epigenetics<br />
|Germany<br />
|Freiburg<br />
|Max Planck Institute of Immunbiology and Epigenetics<br />
|The Max Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany invites applications for the position of a Bioinformatician to start as soon as possible for an initial period of two years, with the possibility of extension.<br />
<br />
Our Institute investigates the molecular basis of the immune response and other topics of the developmental biology, such as the origin and differentiation of the immune cells as well as the develop-ment of vertebrate embryo. Another main focus of the Institute is Epigenetic. This area deals with inheritable traits, which are not caused by changes in the DNA sequence.<br />
|2017-05-02<br />
|manke@ie-freiburg.mpg.de<br />
|[https://euraxess.ec.europa.eu/jobs/165196 job offer]<br />
|-<br />
| PostDoc <br />
|Proteomics|| Denmark || Odense || University of Southern Denmark || The research project entails the systems-level analysis of temporal abundance profiles of proteins and their post-translational modifications (PTMs, e.g. phosphorylation, acetylation). The candidate will develop algorithms and use computational and statistical tools to elucidate the molecular mechanisms and regulatory features that initiate and maintain specific cellular lineages. || 2017-03-29 || veits@bmb.sdu.dk || [https://www.myscience.org/jobs/id683606-postdoctoral_fellowship_in_proteomics-bioinformatics_temporal_profiling_of_functional_control_mechanisms_in_cell_differentiation-university_of_southern_denmark-odense] <br />
<br />
|-<br />
|-<br />
| PostDoc <br />
|Systems Biology|| Germany || Dortmund || ISAS e.V. || ISAS Dortmund seeks a talented and highly motivated computer scientist to pursue bioinformatics network analysis to elucidate novel signalling hubs in insulin resistance within the Leibnitz funded “A Synaptoneurolipidomics View on Neuronal Plasticity in Insulin Resistance and Alzheimer's disease” SAW project. || 2017-01-27 || personal@isas.de || [https://docs.google.com/viewer?a=v&pid=forums&srcid=MDc3MTQ5NzMwMjMwMDM4MTkyNTYBMDkwNTc1NDI4OTA0Njg0MDYzODIBZnBoS1FTaTVGZ0FKATAuMQEBdjI job offer]<br />
|-<br />
|-<br />
| PostDoc <br />
|Lipidomics|| Germany || Dortmund || ISAS e.V. || ISAS Dortmund seeks a talented and highly motivated Bioinformation to pursue bioinformatics infrastructure projects in collaboration within the German Network for Bioinformatics-Infrastructure (de.NBI). The primary focus is the setup of lipidomics search engines and the provision of databases for targeted lipidomics in biomedical research. || 2017-01-27 || personal@isas.de || [https://docs.google.com/viewer?a=v&pid=forums&srcid=MDc3MTQ5NzMwMjMwMDM4MTkyNTYBMDkwNTc1NDI4OTA0Njg0MDYzODIBZnBoS1FTaTVGZ0FKATAuMgEBdjI job offer]<br />
|-<br />
|PostDoc<br />
|Genomics<br />
|Norway<br />
|Bergen<br />
|University of Bergen<br />
|The work is intended to identify novel genes and mechanisms involved in predisposition to abnormal growth, childhood obesity and diabetes. The candidates will mainly work with a unique GWAS and exome chip dataset of 11 000 mother-father-child trios from the population-based Mother and Child Cohort of Norway (MoBa). Tasks will involve associations based studies on genotype-phenotype relationships, application and development of methods for trio-analysis, imputation and rare-coding variant analysis and longitudinal analysis and epidemiology.<br />
|2017-03-27<br />
|stefan.johansson@uib.no<br />
|[https://www.jobbnorge.no/en/available-jobs/job/133818/postdoctoral-fellow-at-the-department-of-clinical-science job offer]<br />
|-<br />
|-<br />
| Scientific Software Designer <br />
|Infrastructure|| Denmark || Odense || University of Southern Denmark || We are now looking for skilled software developers to create a pilot infrastructure for a research cloud service. One of the positions is reserved for a team leader for this project. The project involves the design and development of: a distributed cloud storage service for researchers; an interface to computing infrastructures, such as the national HPC center at SDU; a container system for scientific applications as a cloud computing service integrated with the cloud storage and HPC system. || 2017-02-15 || pica@cp3-origins.net || [https://ssl1.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm?PortalID=3794&VacatureID=879859 job offer]<br />
|-<br />
|PostDoc<br />
|Proteomics<br />
|France<br />
|Grenoble<br />
|CNRS<br />
|Analyses of the phosphoproteome and of histone post-translational modifications (PTMs) by mass spectrometry, of chromatin re-organization by ATAC-sequencing, and of mRNA by RNA-sequencing will be performed on endothelial cells at different time points after application of extracellular vesicles produced by a cancer cell line. the recruited person will carry out bioinformatics analysis of each omics data independently. In proteomics, given the wealth of PTMs modifying histones described over the past ten years, a particular challenge consists of the interpretation of mass spectrometry (MS/MS) spectra by the establishment of a dedicated bioinformatics method. Transcriptomic data will be processed to quantify expression and to detect differentially expressed / spliced transcripts. Then, the recruited person will work on the integrated analysis of these multi-omics processed data to decipher target cell perturbations undergone after internalization of extracellular vesicles secreted by cancer cells.<br />
|2017-02-28<br />
|delphine.pflieger@cea.fr<br />
|[http://www.edyp.fr/index.php/30-jobs/112-data-integration-from-intracellular-phospho-signaling-to-gene-expression-re-programming job offer]<br />
|-<br />
|}<br />
* '''Industry'''<br />
{| class="wikitable"<br />
!Position<br />
!Category<br />
!Country<br />
!City<br />
!Institute<br />
!Description<br />
!Expiring date<br />
!Contact<br />
!Link<br />
|}</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Project:FindABioinformatician&diff=342Project:FindABioinformatician2017-07-04T07:49:12Z<p>Jg: Created project page for FindABioinformatician</p>
<hr />
<div>The '''Find A Bioinformatician''' intends to create a platform for wet-lab scientists to post (descriptions) of datasets to find a collaboration with a bioinformatician to analyse the data.<br />
<br />
== Current Status ==<br />
<br />
This project is still in the planning phase and will probably be developed during the next Winter School meeting.<br />
<br />
== People ==<br />
<br />
* [[User:jg|Johannes Griss]]</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Projects&diff=341Projects2017-07-04T07:47:05Z<p>Jg: Added FindABioinformatician</p>
<hr />
<div>This page gives an overview over all projects currently supported or coordinated by EuBIC.<br />
<br />
All new project pages should be in the '''Project:''' namespace (ie. "Project:TheGreatProject").<br />
<br />
== Community ==<br />
<br />
'''[[Project:JobFair| Job Fair]]:''' <br />
<br />
This project is run in collaboration with the YPIC initiative to create a job portal for proteomics / bioinformatics associated jobs. Further plans exist to implement a "talent pool" where researchers looking for a new job can provide e.g. their CVs.<br />
<br />
'''[[Project:FindABioinformatician| Find A Bioinformatician]]:'''<br />
<br />
This project is intended to create a platform for research groups to post a research question / dataset to find a collaboration with a bioinformatician to analyse the data.<br />
<br />
'''[[Project:HUPO2017| EuBIC activities at HUPO 2017]]'''<br />
<br />
'''[[Project:EUPA2018| EuBIC activities at EUPA 2018]]'''<br />
<br />
Developper meeting 2018<br />
<br />
EuBIC winter school 2019</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Projects&diff=330Projects2017-06-01T08:13:39Z<p>Jg: </p>
<hr />
<div>This page gives an overview over all projects currently supported or coordinated by EuBIC.<br />
<br />
All new project pages should be in the '''Project:''' namespace (ie. "Project:TheGreatProject").<br />
<br />
== Community ==<br />
<br />
* [[Project:JobFair|Job Fair]]: This project is run in collaboration with the EuYPIC initiative to create a job portal for proteomics / bioinformatics associated jobs.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Project:JobFair&diff=329Project:JobFair2017-06-01T08:12:45Z<p>Jg: Job Fair project page</p>
<hr />
<div>The '''Job Fair''' project is run in collaboration with the EuYPIC initiative to create a job portal for proteomics / bioinformatics jobs.<br />
<br />
== Resources ==<br />
<br />
A '''first test''' has been launched as part of this wiki's [[Jobs]] page. Even though this is very rudimentary a surprising number of jobs has already been posted. <br />
<br />
A new system was now set up, available at http://jobs2.proteomics-academy.org that will give us more flexibility. Once this system is completely ready, it will be launched and replace the wiki page.<br />
<br />
== People ==<br />
<br />
* [[User:jg|Johannes Griss]]</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Projects&diff=328Projects2017-06-01T08:08:18Z<p>Jg: </p>
<hr />
<div>This page gives an overview over all projects currently supported or coordinated by EuBIC.<br />
<br />
== Community ==<br />
<br />
* [[Project:JobFair|Job Fair]]: This project is run in collaboration with the EuYPIC initiative to create a job portal for proteomics / bioinformatics associated jobs.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Projects&diff=327Projects2017-06-01T08:08:04Z<p>Jg: </p>
<hr />
<div>This page gives an overview over all projects currently supported or coordinated by EuBIC.<br />
<br />
== Community ==<br />
<br />
* [[Project:JobFair]]: This project is run in collaboration with the EuYPIC initiative to create a job portal for proteomics / bioinformatics associated jobs.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Category:Project&diff=326Category:Project2017-06-01T07:59:40Z<p>Jg: Created page with "'''Category:Project''' collects all project pages that describe projects coordinated or supported by EuBIC. An overview can be found on the Projects page."</p>
<hr />
<div>'''Category:Project''' collects all project pages that describe projects coordinated or supported by EuBIC.<br />
<br />
An overview can be found on the [[Projects]] page.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Projects&diff=325Projects2017-06-01T07:55:31Z<p>Jg: </p>
<hr />
<div>This page gives an overview over all projects currently supported or coordinated by EuBIC.<br />
<br />
== Community ==<br />
<br />
* [[Project:JobFair|Job Fair]]: This project is run in collaboration with the EuYPIC initiative to create a job portal for proteomics / bioinformatics associated jobs.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Projects&diff=324Projects2017-06-01T07:54:44Z<p>Jg: New Projects page created</p>
<hr />
<div>This page gives an overview over all projects currently supported or coordinated by EuBIC.<br />
<br />
== Community ==<br />
<br />
* [[Projet:JobFair|Job Fair]]: This project is run in collaboration with the EuYPIC initiative to create a job portal for proteomics / bioinformatics associated jobs.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Protocols&diff=317Protocols2017-04-20T08:37:58Z<p>Jg: Added links to PrimeXS Protocols</p>
<hr />
<div>Here we try to present different protocols.<br />
<br />
== Internal Resources ==<br />
<br />
== External Resources ==<br />
=== Duke Center for Genomic and Computational Biology ===<br />
<br />
This site provides more than 10 protocols ranging from a basic tryptic digest to phosphopeptide enrichment.<br />
<br />
https://genome.duke.edu/cores-and-services/proteomics-and-metabolomics/protocols-reagents<br />
<br />
=== PrimeXS Protocols ===<br />
A collections of protocols used at the Transnational Access sites of the PRIME-XS project.<br />
<br />
These currently include:<br />
* Determination of protein concentration using the Bradford Assay ([http://www.primexs.eu/protocols/Public-Documents/04---Protocols/PRIME-XS-Protocol-NPC-Bradford-Protein-Assay.pdf/ link])<br />
* Lysis of cells and tissue samples for LC-MS/MS analysis ([http://www.primexs.eu/protocols/Public-Documents/04---Protocols/PRIME-XS-Protocol-NPC-Cell-Lysis.pdf/ link])<br />
* NPC HILIC peptide fractionation ([http://www.primexs.eu/protocols/Public-Documents/04---Protocols/PRIME-XS-Protocol-NPC-HILIC-peptide-fractionation/ link])<br />
* In gel digestion of proteins using trypsin from Coomassie or Silver stained gels ([http://www.primexs.eu/protocols/Public-Documents/04---Protocols/PRIME-XS-Protocol-NPC-In-Gel-Digestion.pdf/ link])<br />
* In-solution digestion of proteins using various different enzymes ([http://www.primexs.eu/protocols/Public-Documents/04---Protocols/PRIME-XS-Protocol-NPC-In-Solution-Digestion.pdf/ link])<br />
* In-solution and in-gel digestion of proteins using Metalloendopeptidase Lys-N ([http://www.primexs.eu/protocols/Public-Documents/04---Protocols/PRIME-XS-Protocol-NPC-Lys-N-Digestion.pdf/ link])<br />
* Stable Isotope Labeling (SILAC) by Amino Acids Applied of Bacterial Cell Cultures ([http://www.primexs.eu/protocols/Public-Documents/04---Protocols/PRIME-XS-Protocol-SILAC-Bacteria.pdf/ link])<br />
* Enrichment of phosphopeptides using titanium dioxide (TiO2) affinity chromatography, for LC-MS/MS analysis ([http://www.primexs.eu/protocols/Public-Documents/04---Protocols/PRIME-XS-Protocol-TiO2-phosphopeptide-enrichment/ link])<br />
The complete list of protocols can be found at http://www.primexs.eu/protocols.html.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Grants&diff=316Grants2017-04-20T08:30:58Z<p>Jg: Updated EuPA Grants</p>
<hr />
<div>This page lists grants available for bioinformaticians focused on the field of proteomics.<br />
<br />
== Travel Grants ==<br />
<br />
{| class="wikitable sortable"<br />
|-<br />
! Name !! Target Audience !! Price !! Description !! Requirements !! Deadline !! Contact !! Link<br />
|-<br />
| EuPA Travel Grant || PhD, PostDoc || Up to 500,00 Euro || For relevant Proteomic conferences 2 EuPA travel grants for each event of up to € 500,00 are available. Travel receipts will be asked in order to justify the requested amount. Participants from Societies other than the local organizers will receive priority. Awardees will be identified by EuPA EC in agreement with a local society representative. || Applicants must meet the following requirements (i) PhD/Master degree ≤ 7 years; (ii) individual member of a EuPA Associated Society; (iii) completed registration for the intended Conference; (iv) submission of an abstract for the Conference || Ongoing || Applications should be sent to the EuPA Secretary, Christian Kleinhammer (c.kleinhammer@aon.at), no later than two weeks before the event. || http://eupa.org<br />
|-<br />
| EuPA Exchange Program || PhD, PostDoc || Up to 1.000,00 Euro || EuPA will subsidize exchange programs of young researchers endorsed by National Societies (including the use of competitively obtained exchange funding) by matching up to € 1’000,00 the amount of the fellowship awarded. This action is dedicated for developing collaborative networks among the different EuPA member communities, minimum 2 EuPA member Societies must support the proposal. New collaborations, dedicated brief experimental sessions and training activities will be prioritized (congress participation is not eligible activity). || Two letters of presentation from two different EuPA societies (signed by the respective legal representatives) stating the amount allocated and a synopsis (1 side A4 paper) of the research proposal should be produce by the applicant. Funds will be transferred to the successful applicant upon acknowledgment of the receiving institution of a letter stating the completion of the proposed activities. Applicants must meet the following requirements (i) PhD/Master degree ≤ 7 years; (ii) individual member of a EuPA Associated Society || Ongoing || Applications should be sent to the EuPA Secretary, Christian Kleinhammer (c.kleinhammer@aon.at), no later than one month before the schedule mission. || http://eupa.org<br />
|}<br />
<br />
== Other grants ==<br />
<br />
No grants listed<br />
<br />
== How to post a grant ==<br />
<br />
To post a grant on this site, simply register for this wiki and edit this page. When adding new grants please adhere to these guidelines:<br />
<br />
* '''Name''': The (short) name of the grant<br />
* '''Target Audience''': The group of people who should apply for this grant, ie. "PhD", "PostDoc", "all"<br />
* '''Price''': A short description of what will be awarded.<br />
* '''Description''': A short description about the grant's objective<br />
* '''Requirements''': A short list of requirements the applicant has to fulfil to apply for this grant<br />
* '''Deadline''': Date until which the application must be submitted<br />
* '''Contact''': The primary contact for this grant<br />
* '''Link''': Link pointing to the official grant's page</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=MediaWiki:Sidebar&diff=295MediaWiki:Sidebar2017-01-25T10:57:13Z<p>Jg: </p>
<hr />
<div><br />
* navigation<br />
** mainpage|Proteomics Academy<br />
* Education<br />
** Courses|Courses<br />
** Tutorials|Tutorials<br />
** Educational Videos|Educational Videos<br />
** Protocols|Protocols<br />
* Service<br />
** Jobs|Jobs<br />
** Grants|Grants<br />
* External Links<br />
** http://www.proteomics-academy.org/|Proteomics Academy<br />
** http://www.eupa.org|EuPA<br />
* Site Information<br />
** recentchanges-url|recentchanges<br />
** helppage|help<br />
* SEARCH<br />
* TOOLBOX<br />
* LANGUAGES</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=MediaWiki:Sidebar&diff=294MediaWiki:Sidebar2017-01-25T10:56:39Z<p>Jg: Added Protocols and Jobs + Grants page</p>
<hr />
<div><br />
* navigation<br />
** mainpage|Proteomics Academy<br />
* Education<br />
** Courses|Courses<br />
** Tutorials|Tutorials<br />
** Educational Videos|Educational Videos<br />
** Protocols|Protocols<br />
* Service<br />
** Job Listings|Jobs<br />
** Grants|Grants<br />
* External Links<br />
** http://www.proteomics-academy.org/|Proteomics Academy<br />
** http://www.eupa.org|EuPA<br />
* Site Information<br />
** recentchanges-url|recentchanges<br />
** helppage|help<br />
* SEARCH<br />
* TOOLBOX<br />
* LANGUAGES</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Main_Page&diff=292Main Page2017-01-25T10:53:52Z<p>Jg: Added links to logos</p>
<hr />
<div>= Proteomics Academy by EuBIC and EuPA =<br />
<br />
[[File:Eubic_logo.png|x120px|link=http://www.proteomics-academy.org]][[File:Eupa_logo.png|x120px|right|link=http://www.eupa.org]]<br />
<br />
The Proteomics Academy is an education platform created by the the [http://www.eupa.org/ European Proteomics Association (EuPA)] educational committee and the [http://www.proteomics-academy.org European Bioinformatics Community (EuBIC)] initiative to foster exchange of knowledge on proteomics. We organize training events throughout Europe and provide as many of the used training materials on this website.<br />
<br />
People involved in the European Proteomics Academy including scientific advisory board and the education committee can be found [[European Proteomics Academy:People|here]].<br />
<br />
<br />
== Courses ==<br />
<br />
The [http://eupa.org EuPA] organizes proteomics courses through Europe.<br />
<br />
The [[EuPA:Courses]] section provides a complete list of courses.<br />
<br />
<br />
== Tutorials ==<br />
<br />
You will find in this section a selection of online free tutorials to learn more about proteomics.<br />
<br />
The [[Tutorials]] section provides the entry point to all tutorials found on this site.<br />
<br />
<br />
== Educational Videos ==<br />
<br />
You will find in this section a selection of online videos to learn more about proteomics.<br />
<br />
The [[Educational Videos]] section provides the entry point to all educational videos found on this site.<br />
<br />
== Protocols ==<br />
<br />
You will find in this section a selection of protocols to prime your experiments.<br />
<br />
The [[Protocols]] section provides the entry point to all protocols found on this site.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Main_Page&diff=291Main Page2017-01-25T10:51:31Z<p>Jg: Added EuBIC logo</p>
<hr />
<div>= Proteomics Academy by EuBIC and EuPA =<br />
<br />
[[File:Eubic_logo.png|x120px]][[File:Eupa_logo.png|x120px|right]]<br />
<br />
The Proteomics Academy is an education platform created by the the [http://www.eupa.org/ European Proteomics Association (EuPA)] educational committee and the [http://www.proteomics-academy.org European Bioinformatics Community (EuBIC)] initiative to foster exchange of knowledge on proteomics. We organize training events throughout Europe and provide as many of the used training materials on this website.<br />
<br />
People involved in the European Proteomics Academy including scientific advisory board and the education committee can be found [[European Proteomics Academy:People|here]].<br />
<br />
<br />
== Courses ==<br />
<br />
The [http://eupa.org EuPA] organizes proteomics courses through Europe.<br />
<br />
The [[EuPA:Courses]] section provides a complete list of courses.<br />
<br />
<br />
== Tutorials ==<br />
<br />
You will find in this section a selection of online free tutorials to learn more about proteomics.<br />
<br />
The [[Tutorials]] section provides the entry point to all tutorials found on this site.<br />
<br />
<br />
== Educational Videos ==<br />
<br />
You will find in this section a selection of online videos to learn more about proteomics.<br />
<br />
The [[Educational Videos]] section provides the entry point to all educational videos found on this site.<br />
<br />
== Protocols ==<br />
<br />
You will find in this section a selection of protocols to prime your experiments.<br />
<br />
The [[Protocols]] section provides the entry point to all protocols found on this site.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=File:Eubic_logo.png&diff=290File:Eubic logo.png2017-01-25T10:41:43Z<p>Jg: </p>
<hr />
<div></div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Main_Page&diff=289Main Page2017-01-25T10:39:43Z<p>Jg: Added reference to EuBIC</p>
<hr />
<div>= Proteomics Academy by EuBIC and EuPA =<br />
<br />
[[File:Eupa_logo.png|x120px|center]]<br />
<br />
The Proteomics Academy is an education platform created by the the [http://www.eupa.org/ European Proteomics Association (EuPA)] educational committee and the [http://www.proteomics-academy.org European Bioinformatics Community (EuBIC)] initiative to foster exchange of knowledge on proteomics. We organize training events throughout Europe and provide as many of the used training materials on this website.<br />
<br />
People involved in the European Proteomics Academy including scientific advisory board and the education committee can be found [[European Proteomics Academy:People|here]].<br />
<br />
<br />
== Courses ==<br />
<br />
The [http://eupa.org EuPA] organizes proteomics courses through Europe.<br />
<br />
The [[EuPA:Courses]] section provides a complete list of courses.<br />
<br />
<br />
== Tutorials ==<br />
<br />
You will find in this section a selection of online free tutorials to learn more about proteomics.<br />
<br />
The [[Tutorials]] section provides the entry point to all tutorials found on this site.<br />
<br />
<br />
== Educational Videos ==<br />
<br />
You will find in this section a selection of online videos to learn more about proteomics.<br />
<br />
The [[Educational Videos]] section provides the entry point to all educational videos found on this site.<br />
<br />
== Protocols ==<br />
<br />
You will find in this section a selection of protocols to prime your experiments.<br />
<br />
The [[Protocols]] section provides the entry point to all protocols found on this site.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Jobs&diff=285Jobs2017-01-24T09:35:14Z<p>Jg: Added TOC</p>
<hr />
<div>__FORCETOC__<br />
<br />
This page is a collection of job advertisements focused on people with bioinformatics expertise. To post a job, simply edit this page.<br />
<br />
== Academia ==<br />
<br />
{| class="wikitable sortable"<br />
|-<br />
! Position !! Country !! City !! Institute !! Description !! Expiring date !! Contact !! Link <br />
|-<br />
| PostDoc || Denmark || Copenhagen || University of Southern Denmark || The research project entails the systems-level analysis of temporal abundance profiles of proteins and their post-translational modifications (PTMs, e.g. phosphorylation, acetylation). The candidate will develop algorithms and use computational and statistical tools to elucidate the molecular mechanisms and regulatory features that initiate and maintain specific cellular lineages. || || veits@bmb.sdu.dk || http://jobbank.sdu.dk/job/934815<br />
|-<br />
|-<br />
| PostDoc || Germany || Dortmund || ISAS e.V. || ISAS Dortmund seeks a talented and highly motivated computer scientist to pursue bioinformatics network analysis to elucidate novel signalling hubs in insulin resistance within the Leibnitz funded “A Synaptoneurolipidomics View on Neuronal Plasticity in Insulin Resistance and Alzheimer's disease” SAW project. || January 27th 2017 || personal@isas.de || [https://docs.google.com/viewer?a=v&pid=forums&srcid=MDc3MTQ5NzMwMjMwMDM4MTkyNTYBMDkwNTc1NDI4OTA0Njg0MDYzODIBZnBoS1FTaTVGZ0FKATAuMQEBdjI job offer]<br />
|-<br />
|-<br />
| PostDoc || Germany || Dortmund || ISAS e.V. || ISAS Dortmund seeks a talented and highly motivated Bioinformation to pursue bioinformatics infrastructure projects in collaboration within the German Network for Bioinformatics-Infrastructure (de.NBI). The primary focus is the setup of lipidomics search engines and the provision of databases for targeted lipidomics in biomedical research. || January 27th 2017 || personal@isas.de || [https://docs.google.com/viewer?a=v&pid=forums&srcid=MDc3MTQ5NzMwMjMwMDM4MTkyNTYBMDkwNTc1NDI4OTA0Njg0MDYzODIBZnBoS1FTaTVGZ0FKATAuMgEBdjI job offer]<br />
|-<br />
|}<br />
<br />
== Industry ==<br />
<br />
No posted jobs<br />
<br />
== How to post a job ==<br />
<br />
If you are interested in posting a job, simply register for this wiki and edit this page.<br />
<br />
The fields in the table should be filled out according to these guidelines:<br />
* '''Position''': PhD, PostDoc, Staff scientist, Group leader<br />
* '''Country''': Name of the country written out (Belgium, Austria)<br />
* '''Institute''': The institute's (short) name<br />
* '''Description''': A very short description about the main requirements for this job and the main duties. This should not be a detailed job description but only a short summary.<br />
* '''Contact''': Primary means of contact for this job offer<br />
* '''Link''': Link to the official job posting at your institute's website.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Grants&diff=284Grants2017-01-24T08:51:49Z<p>Jg: First draft of the grants page</p>
<hr />
<div>This page lists grants available for bioinformaticians focused on the field of proteomics.<br />
<br />
== Travel Grants ==<br />
<br />
{| class="wikitable sortable"<br />
|-<br />
! Name !! Target Audience !! Price !! Description !! Requirements !! Deadline !! Contact !! Link<br />
|-<br />
| EuPA Travel Grant || PhD, PostDoc || Up to 100,00 Euro || This grant is supporting short research stays (ie. a few weeks) of young scientists in another European lab || Existing funding for the research stay will be matched by EuPA. This funding must be approved by the local proteomics initiative which must be a member of EuPA || Ongoing || info@eupa.org || http://eupa.org<br />
|}<br />
<br />
== Other grants ==<br />
<br />
No grants listed<br />
<br />
== How to post a grant ==<br />
<br />
To post a grant on this site, simply register for this wiki and edit this page. When adding new grants please adhere to these guidelines:<br />
<br />
* '''Name''': The (short) name of the grant<br />
* '''Target Audience''': The group of people who should apply for this grant, ie. "PhD", "PostDoc", "all"<br />
* '''Price''': A short description of what will be awarded.<br />
* '''Description''': A short description about the grant's objective<br />
* '''Requirements''': A short list of requirements the applicant has to fulfil to apply for this grant<br />
* '''Deadline''': Date until which the application must be submitted<br />
* '''Contact''': The primary contact for this grant<br />
* '''Link''': Link pointing to the official grant's page</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Jobs&diff=281Jobs2017-01-23T21:59:52Z<p>Jg: First draft of a job page</p>
<hr />
<div>This page is a collection of job advertisements focused on people with bioinformatics expertise.<br />
<br />
== Academia ==<br />
<br />
{| class="wikitable sortable"<br />
|-<br />
! Position !! Country !! City !! Institute !! Description !! Contact !! Link <br />
|-<br />
| PostDoc || Denmark || Copenhagen || University of Southern Denmark || The research project entails the systems-level analysis of temporal abundance profiles of proteins and their post-translational modifications (PTMs, e.g. phosphorylation, acetylation). The candidate will develop algorithms and use computational and statistical tools to elucidate the molecular mechanisms and regulatory features that initiate and maintain specific cellular lineages. || veits@bmb.sdu.dk || http://jobbank.sdu.dk/job/934815<br />
|-<br />
|}<br />
<br />
== Industry ==<br />
<br />
No posted jobs<br />
<br />
== How to post a job ==<br />
<br />
If you are interested in posting a job, simply register for this wiki and edit this page.<br />
<br />
The fields in the table should be filled out according to these guidelines:<br />
* '''Position''': PhD, PostDoc, Staff scientist, Group leader<br />
* '''Country''': Name of the country written out (Belgium, Austria)<br />
* '''Institute''': The institute's (short) name<br />
* '''Description''': A very short description about the main requirements for this job and the main duties. This should not be a detailed job description but only a short summary.<br />
* '''Contact''': Primary means of contact for this job offer<br />
* '''Link''': Link to the official job posting at your institute's website.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Spectra-cluster-cli&diff=280Spectra-cluster-cli2017-01-23T21:43:38Z<p>Jg: </p>
<hr />
<div>{{Infobox searchengine<br />
| author = J. Griss, R. Wang<br />
| name = spectra-cluster-cli<br />
| website = https://github.com/spectra-cluster/spectra-cluster-cli<br />
| released = 15.03.2016<br />
| operating_system = Windows, Linux, Mac OSX<br />
| input = MGF<br />
| output = [[.clustering]]<br />
| status = active<br />
| license = [http://www.apache.org/licenses/LICENSE-2.0.html Apache 2]<br />
}}<br />
<br />
The spectra-cluster-cli is a stand-alone, command-line version of the [https://www.github.com/spectra-cluster/spectra-cluster spectra-cluster] algorithm to cluster MS/MS spectra. The spectra-cluster algorithm is used to create the [https://www.ebi.ac.uk/pride/cluster PRIDE Cluster] resource. The spectra-cluster-cli tool allows user to cluster their own MS/MS data on a normal computer.<br />
<br />
== Features ==<br />
<br />
The spectra-cluster-cli is a command-line tool. It clusters MS/MS spectra in the [[MGF]] peak list format and writes the results to a [[.clustering]] result file. It currently supports:<br />
* Clustering of MS/MS spectra ([[MGF]] format)<br />
* Parallel processing of data<br />
<br />
'''Note''': Alternatively, a graphical user interface is also available at https://github.com/spectra-cluster/spectra-cluster-gui<br />
<br />
Additionally, you can find a detailed example of how to prepare your data for clustering at http://spectra-cluster.github.io.<br />
<br />
== Installation ==<br />
<br />
=== Requirements ===<br />
<br />
To run the spectra-cluster-cli [https://www.oracle.com/java/index.html Java] needs to be installed on the computer.<br />
<br />
=== Downloading spectra-cluster-cli ===<br />
<br />
# Download the latest release from [https://github.com/spectra-cluster/spectra-cluster-cli/releases https://github.com/spectra-cluster/spectra-cluster-cli/releases]<br />
# Unpack the downloaded zip file. No further installation is required<br />
<br />
== Usage ==<br />
<br />
=== Preparing your data ===<br />
<br />
Peak lists must be available in [[MGF]] format. In case your data is only available in a different format, use [http://proteowizard.sourceforge.net/downloads.shtml ProteoWizard's msconvert] to convert it to [[MGF]].<br />
<br />
Optionally, identification data can be incorporated into the [[MGF]] files using the <code>SEQ=</code> tag. A tool to do this automatically is under active development and will be released shortly. The identification data does not influence the clustering process. If identification data is present in the used [[MGF]] files the corresponding data will automatically be written to the resulting [[.clustering]] files.<br />
<br />
=== Performing the clustering ===<br />
<br />
==== Summary ====<br />
<syntaxhighlight lang="bat"><br />
C:\>cd C:\Downloads\spectra-cluster-cli<br />
C:\Downloads\spectra-cluster-cli>java -jar spectra-cluster-cli-1.0-SNAPSHOT.jar -rounds 4 -threshold_end 0.99 -threshold_start 0.9999 -output_path C:\my_data\clustering_results.clustering C:\my_data\peaklists\*.mgf<br />
</syntaxhighlight><br />
<br />
==== Detailed instructions ====<br />
<br />
# Open a command prompt. On windows this is achieved by opening the <code>run</code> dialog, entering "cmd" and clicking enter (on Windows 7 simply click the windows key and immediately enter "cmd").<br />
# Navigate to the directory where you downloaded the spectra-cluster-cli tool.<br />
# Launch the spectra-cluster-cli through the command <code>java -jar spectra-cluster-cli-1.0-SNAPSHOT.jar</code> (see above). '''Note:''' the <code>spectra-cluster-cli-1.0-SNAPSHOT.jar</code> part has to be adapted based on the downloaded version.<br />
<br />
==== Additional options ====<br />
<syntaxhighlight><br />
-binary_directory <arg> path to the directory to<br />
(temporarily) store the binary<br />
files. By default a temporary<br />
directory is being created<br />
-cluster_binary_file <arg> if this option is set, only the<br />
passed binary file will be<br />
clustered and the result written<br />
to the file specified in<br />
'-output_path' in the binary<br />
format<br />
-convert_cgf if this option is set the passed<br />
CGF file is converted into a<br />
.clustering file<br />
-fast_mode if this option is set the 'fast<br />
mode' is enabled. In this mode,<br />
the radical peak filtering used<br />
for the comparison function is<br />
already applied during spectrum<br />
conversion. Thereby, the<br />
clustering and consensus spectrum<br />
quality is slightly decreased but<br />
speed increases 2-3 fold.<br />
-fragment_tolerance fragment ion tolerance in m/z to<br />
use for fragment peak matching<br />
-help print this message.<br />
-keep_binary_files if this options is set, the<br />
binary files are not deleted<br />
after clustering.<br />
-major_peak_jobs <arg> number of threads to use for<br />
major peak clustering.<br />
-merge_binary_results if this option is set, the passed<br />
binary results files are merged<br />
into a single .cgf file and<br />
written to '-output_path'<br />
-output_path <arg> path to the outputfile.<br />
Outputfile must not exist.<br />
-precursor_tolerance <arg> precursor tolerance (clustering<br />
window size) in m/z used during<br />
matching.<br />
-reuse_binary_files if this option is set, the binary<br />
files found in the binary file<br />
directory will be used for<br />
clustering.<br />
-rounds <arg> number of clustering rounds to<br />
use.<br />
-threshold_end <arg> (lowest) final clustering<br />
threshold<br />
-threshold_start <arg> (highest) starting threshold<br />
-x_learn_cdf <output filename> (Experimental option) Learn the<br />
used cumulative distribution<br />
function directly from the<br />
processed data. This is only<br />
recommended for high-resolution<br />
data. The result will be written<br />
to the defined file.<br />
-x_load_cdf <CDF filename> (Experimental option) Loads the<br />
cumulative distribution function<br />
to use from the specified file.<br />
These files can be created using<br />
the x_learn_cdf parameter<br />
-x_min_comparisons <arg> (Experimental option) Sets the<br />
minimum number of comparisons<br />
used to calculate the probability<br />
that incorrect spectra are<br />
clustered.<br />
-x_n_prefiltered_peaks <number peaks> (Experimental option) Set the<br />
number of highest peaks that are<br />
kept per spectrum during loading.<br />
</syntaxhighlight><br />
<br />
== Analysing clustering results ==<br />
<br />
We are currently working on an analysis software for clustering results in the [[.clustering]] format.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Spectra-cluster_API&diff=272Spectra-cluster API2016-07-05T09:39:57Z<p>Jg: Created page with "{{Infobox searchengine | author = J. Griss, R. Wang, S. Lewis and J. A. Vizcaíno | name = spectra-cluster API | website = https://gith..."</p>
<hr />
<div>{{Infobox searchengine<br />
| author = J. Griss, R. Wang, S. Lewis and J. A. Vizcaíno<br />
| name = spectra-cluster API<br />
| website = https://github.com/spectra-cluster/spectra-cluster<br />
| released = 24.10.2015<br />
| operating_system = Windows, OS X, Linux<br />
| input = peak list file format, preferred [[MGF]]<br />
| output = [[.clustering]], .cgf (text and binary)<br />
| status = active<br />
| license = Apache License, Version 2.0<br />
}}<br />
<br />
The [[spectra-cluster API]] is a Java application programming interface that supports the rapid development of MS/MS clustering algorithms. It forms the basis of the [https://github.com/spectra-cluster/spectra-cluster-hadoop spectra-cluster-hadoop] implementation of the spectra-cluster algorithm used to create the [https://www.ebi.ac.uk/pride/cluster PRIDE Cluster] resource<ref>Griss, J et al., Nat Methods. 2016, [http://rdcu.be/i1Sa doi:10.1038/nmeth.3902]</ref>. Additionally, it is used by the [[spectra-cluster-cli]] command-line tool and the [[spectra-cluster-gui]] GUI application to implement the spectra-cluster algorithm as stand-alone applications.<br />
<br />
== General concept ==<br />
<br />
The [[spectra-cluster API]] represents each vital component of a MS/MS clustering algorithm as a Java interface. Thereby, if a developer is only interested in developing a new spectrum similarity metric, he or she only has to implement the respective interface and can immediately put his algorithm in production by adapting, for example, the [[spectra-cluster-cli]].<br />
<br />
== References ==</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Test:Boxed_main_page&diff=221Test:Boxed main page2016-06-19T20:03:12Z<p>Jg: </p>
<hr />
<div>'''This is only a test page to test some layout features'''<br />
<br />
[[File:Eupa_logo.png|x200px|center]]<br />
<br />
{{Main page box|Welcome!|Main Page}}<br />
<div style="margin: -0.3em -1em -1em -1em;"><br />
{| width="100%" bgcolor="#fff" border="0" cellpadding="2px" cellspacing="2px" style="margin:auto;"<br />
|- align="center" bgcolor="#e7eef6"<br />
! width="33%" | '''Finding help'''<br />
! width="34%"| '''EuPA Courses'''<br />
! width="33%"| '''Contributing to the Wiki'''<br />
|- valign="top" align="left" style="background: #F5FAFF;"<br />
| Use the search box on the top right to search for your topic of interest.<br />
| All courses can be found at http://www.proteomics-academy.org.<br />
| Simply enter our software's name in the search box and create the page. If you are not registered yet, simply register by clicking the Login link.<br />
|}<br />
</div><br />
{{box-footer-empty}}</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Test:Boxed_main_page&diff=220Test:Boxed main page2016-06-19T07:28:39Z<p>Jg: Testing new layouts</p>
<hr />
<div>'''This is only a test page to test some layout features'''<br />
<br />
{{Main page box|Welcome!|Main Page}}<br />
<div style="margin: -.3em -1em -1em -1em;"><br />
{| width="100%" bgcolor="#fff" border="0" cellpadding="2px" cellspacing="2px" style="margin:auto;"<br />
|- align="center" bgcolor="#e7eef6"<br />
! width="33%" | '''Finding help'''<br />
! width="34%"| '''EuPA Courses'''<br />
! width="33%"| '''Contributing to the Wiki'''<br />
|- valign="top" align="left" style="background: #F5FAFF;"<br />
| Use the search box on the top right to search for your topic of interest.<br />
| All courses can be found at [http://www.proteomics-academy.org].<br />
| Simply enter our software's name in the search box and create the page. If you are not registered yet, simply register by clicking the Login link.<br />
|}<br />
</div><br />
{{box-footer-empty}}</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=User:Jg&diff=219User:Jg2016-06-19T07:16:13Z<p>Jg: </p>
<hr />
<div>Currently a resident at the [http://www.meduniwien.ac.at Medical University of Vienna], previously part of the [https://www.ebi.ac.uk/pride PRIDE team] at the [https://www.ebi.ac.uk EMBL-EBI].<br />
<br />
== Research interests ==<br />
* Spectrum clustering<br />
** Developer of the [[spectra-cluster-cli]]<br />
** Developer of [https://www.ebi.ac.uk/pride/cluster PRIDE Cluster]<br />
* Unidentified spectra<br />
* Melanoma research<br />
** Combining genomics with proteomics data<br />
<br />
== Test pages ==<br />
* [[User:Jg:Boxed main page|Test for a boxed main page]]<br />
<br />
== Links ==<br />
* [https://www.researchgate.net/profile/Johannes_Griss/publications Research Gate]</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=User:Jg&diff=218User:Jg2016-06-19T07:14:45Z<p>Jg: Created page with "Currently a resident at the [http://www.meduniwien.ac.at Medical University of Vienna], previously part of the [https://www.ebi.ac.uk/pride PRIDE team] at the [https://www.ebi..."</p>
<hr />
<div>Currently a resident at the [http://www.meduniwien.ac.at Medical University of Vienna], previously part of the [https://www.ebi.ac.uk/pride PRIDE team] at the [https://www.ebi.ac.uk EMBL-EBI].<br />
<br />
== Research interests ==<br />
* Spectrum clustering<br />
** Developer of the [[spectra-cluster-cli]]<br />
** Developer of [https://www.ebi.ac.uk/pride/cluster PRIDE Cluster]<br />
* Unidentified spectra<br />
* Melanoma research<br />
** Combining genomics with proteomics data<br />
<br />
== Links ==<br />
* [https://www.researchgate.net/profile/Johannes_Griss/publications Research Gate]</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Template:Main_page_box&diff=217Template:Main page box2016-06-19T07:05:59Z<p>Jg: Created page with "{{Box-header{{{watch|}}} | title={{{1}}} |editpage={{{2}}} |border=#A3B1BF <!-- H210 S15 V75 the color of the borders around Box Sections --> |titleforeground=blac..."</p>
<hr />
<div>{{Box-header{{{watch|}}} | title={{{1}}} <br />
|editpage={{{2}}} <br />
|border=#A3B1BF <!-- H210 S15 V75 the color of the borders around Box Sections --><br />
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|foreground=black}} <!-- This is the color of the Box Section text --><br />
<noinclude>{{Box-footer}}</noinclude></div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Template:Box-header&diff=216Template:Box-header2016-06-19T07:04:14Z<p>Jg: Created page with "<div style="clear: both; <!-- -->position: relative; <!-- -->border: {{{border-type|solid}}} {{{titleborder|{{{border|#ababab}}}}}}; <!-- -->border-..."</p>
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<div><div style="clear: both; <!--<br />
-->position: relative; <!--<br />
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<span class="plainlinks" <!--<br />
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</span>}}<!-- endif EDITLINK<br />
-->{{#if: {{{SPAN|}}} |<span style="font-size:{{{title-font-size|100%}}}; font-weight:bold; margin: 0; padding:0; padding-bottom:.1em; color:{{{titleforeground|#000}}};{{{extra|}}}">{{{title}}}</span>|<h2 style="font-size:{{{title-font-size|100%}}}; font-weight:bold; border: none; margin: 0; padding:0; padding-bottom:.1em; color:{{{titleforeground|#000}}};{{{extra|}}}">{{{title}}}</h2>}}<br />
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<div style="display:block; border: {{{border-width|1}}}px solid {{{border|#ababab}}}; <!--<br />
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-->padding-top: {{{padding-top|.3em;}}}"><!--<br />
--><!--{{#if: {{{TOC|}}} | |__NOTOC__}}{{#if: {{{EDIT|}}} | |__NOEDITSECTION__}}--><noinclude><br />
{{box-footer}}<br />
<br />
{{Documentation}}<br />
</noinclude></div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Template:Box-footer-empty&diff=215Template:Box-footer-empty2016-06-19T07:03:11Z<p>Jg: Created page with "<includeonly><div style="clear:both;"></div></div></includeonly>"</p>
<hr />
<div><includeonly><div style="clear:both;"></div></div></includeonly></div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=European_Proteomics_Academy:People&diff=214European Proteomics Academy:People2016-06-19T07:00:29Z<p>Jg: Updated EC members</p>
<hr />
<div>= Education Committee - Scientific Advisory Board =<br />
<br />
[mailto:mmann@biochem.mpg.de Mathias Mann], Max Planck Institute Munich<br />
<br />
[mailto:a.j.r.heck@uu.nl Albert Heck], Utrecht University<br />
<br />
[mailto:n-kelleher@northwestern.edu Neil Kelleher, Northwestern University], Chicago, USA<br />
<br />
= Education Committee =<br />
[mailto:Rene.zahedi@isas.de Rene Zahedi] – ISAS, Dortmund DE<br />
<br />
[mailto:kai.stuehler@hhu.de Kai Stühler] – Heinrich Heine Universität Düsseldorf , DE<br />
<br />
[mailto:manuel.mayr@kcl.ac.uk Manuel Mayr] – Kings College London, UK<br />
<br />
[mailto:marc.vaudel@biomed.uib.no Marc Vaudel] – University of Bergen, Norway<br />
<br />
[mailto:paola.picotti@bc.biol.ethz.ch Paula Picotti] – ETH, Zurich; Switzerland<br />
<br />
[mailto:eduard.sabido@crg.eu Eduard Sabido] – CRG Barcelona, Spain<br />
<br />
[mailto:Aysel.Ozpinar@acibadem.edu.tr Aysel Ozpinar], Istanbul Üniversitesi, Turkey<br />
<br />
[mailto:tuula.nyman@helsinki.fi Tuula Nyman], Institute of Biotechnology, Helsinki<br />
<br />
[mailto:mechtler@imp.ac.at Karl Mechtler], IMP; Vienna, Austria<br />
<br />
[mailto:johannes.griss@meduniwien.ac.at Johannes Griss], Medical University of Vienna; Austria</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Main_Page&diff=213Main Page2016-06-15T08:02:25Z<p>Jg: Changed details links for courses</p>
<hr />
<div>= European Proteomics Academy =<br />
<br />
[[File:Eupa_logo.png|x200px|center]]<br />
<br />
The European Proteomics Academy is an education platform of the [http://eupa.org European Proteomics Association (EuPA)]. We organize training events throughout Europe and provide as many of the used training materials on this website.<br />
<br />
People involved in the European Proteomics Academy including scientific advisery board and the education committee can be found [[European Proteomics Academy:People|here]].<br />
<br />
== Courses ==<br />
<br />
The [http://eupa.org EuPA] organizes proteomics courses through Europe.<br />
<br />
{| class="wikitable"<br />
|+ Upcoming EuPA Courses<br />
! Title !!Date !!Location<br />
|-<br />
|EuPA Educational Day || 22.06.2016 || EuPA 2016, Istanbul, Turkey<br />
|-<br />
|EuPA BioInformatic Winter School Semmering || 11 - 13.01.2017 || Sermmering, Austria<br />
|}<br />
<br />
'''[[EuPA:Courses|Details and complete list of courses]]'''<br />
<br />
== Tutorials ==<br />
<br />
We try to provide a high-quality selection of tutorials and information materials that should assist anyone interested in proteomics to learn more about the field.<br />
<br />
The [[Tutorials]] section provides the entry point to all tutorials found on this site.<br />
<br />
{| class="wikitable"<br />
|+ Popular Video Tutorials<br />
! Title !!Category !!Description<br />
|-<br />
|[[Tutorial:What is Proteomics|What is Proteomics]] || Beginner<br />
|-<br />
|[[Tutorial:9th European Summer School|9th European Summer School]] || Beginner / Intermediate || These are all lectures held at the 9th European Summer School in 2015<br />
|}</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Courses&diff=212Courses2016-06-15T07:59:56Z<p>Jg: Added Bioinformatic Winter School conference website link</p>
<hr />
<div>== Eductational Day at the EuPA 2016 ==<br />
'''Date:''' Wednesday, 22 June 2016, 08:30-15:30<br />
<br />
'''Location:''' [http://www.eupa2016.org EuPA 2016], Turkey, Istanbul<br />
<br />
The EuPA Educational Day features 4 workshops:<br />
* [http://www.eupa2016.org/workshop1.html Proteomics Bioinformatics Workshop - Basic Level]<br />
* [http://www.eupa2016.org/workshop1.html Proteomics Bioinformatics Workshop - Advanced Level]<br />
* [http://www.eupa2016.org/workshop2.html Variations and Standardization in Proteomics Workshop]<br />
* [http://www.eupa2016.org/workshop3.html Cross-linking Workshop: When Proteomics Meets Structural Biology]<br />
<br />
== EuPA BioInformatic Winter School Semmering 2017 ==<br />
[[image:Semmering.jpg|thumb|right|300px|View of the Semmering railway in summer|link=https://commons.wikimedia.org/wiki/Category:Semmering#/media/File:Semmering_-_Semmeringbahn_mit_Streckenw%C3%A4rterh%C3%A4uschen_und_Kartnerkogel-Tunnel_-_im_Hintergrund_der_Schneeberg.jpg]]<br />
<br />
'''Date:''' 11. - 13. January 2017<br />
<br />
'''Location:''' [https://en.wikivoyage.org/wiki/Semmering Semmering], Austria<br />
<br />
'''Conference details / website''': http://www.fh-ooe.at/eubic-ws17<br />
<br />
This workshop focuses on bioinformatics in proteomics. The first MidWinder Bioinformatics Seminar held in January 2015 brought together leading bioinformaticians from around the world and joined them in the (very) small town of [https://en.wikivoyage.org/wiki/Semmering Semmering].<br />
<br />
This workshop addresses both, beginners and experts who are invited to meet and discuss in a very informal setting.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Template:Infobox_searchengine&diff=211Template:Infobox searchengine2016-06-06T12:50:47Z<p>Jg: Made PMID field optional.</p>
<hr />
<div>{{Infobox<br />
| bodyclass = vevent<br />
| bodystyle = {{{bodystyle|}}}<br />
| title = {{#if:{{{title|{{{name|}}}}}}|{{{title|{{{name|}}}}}}|<includeonly>{{PAGENAME}}</includeonly>}}<br />
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| image = {{#invoke:InfoboxImage|InfoboxImage|image={{{logo|}}}|size={{{logo size|{{{logo_size|}}}}}}|sizedefault=64px|alt={{{logo alt|{{{logo_alt|}}}}}}}}<br />
| caption = {{{logo caption|}}}<br />
| image2 = {{#if:{{{collapsible|}}}|{{hidden begin|title=Screenshot|titlestyle=text-align:center|contentstyle=text-align:center}}}}<br />
| label1 = Original author(s)<br />
| data1 = {{{author|}}}<br />
| label2 = Citation<br />
| data2 = {{{citation|}}}<br />
| label3 = PMID<br />
| data3 = {{#if:{{{pmid|}}}{{PMID|{{{pmid}}}}} }}<br />
| header10 = Usage Details<br />
| label11 = Input format<br />
| data11 = {{{input|}}}<br />
| label12 = Output format<br />
| data12 = {{{output|}}}<br />
| header20 = Software Details<br />
| label21 = Website<br />
| data21 = {{#if:{{{website|}}}<br />
|{{#ifeq:{{{website|}}}|hide||{{{website|}}} }}<br />
|{{#if:{{#property:P856}}<br />
|{{URL|{{#property:P856}}}}<br />
}}<br />
}}<br />
| label22 = Operating system<br />
| data22 = {{{operating_system|}}}<br />
| label23 = [[Computing platform|Platform]]<br />
| data23 = {{{platform|}}}<br />
| label24 = License<br />
| data24 = {{{license|}}}<br />
| label25 = Initial release<br />
| data25 = {{{released|}}}<br />
| label26 = Development status<br />
| data26 = {{{status|}}}<br />
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| data27 = {{{programming_language|}}}<br />
}}<noinclude><br />
{{documentation }}<br />
</noinclude></div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Spectra-cluster-cli&diff=210Spectra-cluster-cli2016-06-06T12:48:00Z<p>Jg: Created page with "{{Infobox searchengine | author = J. Griss, R. Wang | name = spectra-cluster-cli | website = https://github.com/spectra-cluster/spectra..."</p>
<hr />
<div>{{Infobox searchengine<br />
| author = J. Griss, R. Wang<br />
| name = spectra-cluster-cli<br />
| website = https://github.com/spectra-cluster/spectra-cluster-cli<br />
| released = 15.03.2016<br />
| operating_system = Windows, Linux, Mac OSX<br />
| input = MGF<br />
| output = [[.clustering]]<br />
| status = active<br />
| license = [http://www.apache.org/licenses/LICENSE-2.0.html Apache 2]<br />
}}<br />
<br />
The spectra-cluster-cli is a stand-alone, command-line version of the [https://www.github.com/spectra-cluster/spectra-cluster spectra-cluster] algorithm to cluster MS/MS spectra. The spectra-cluster algorithm is used to create the [https://www.ebi.ac.uk/pride/cluster PRIDE Cluster] resource. The spectra-cluster-cli tool allows user to cluster their own MS/MS data on a normal computer.<br />
<br />
== Features ==<br />
<br />
The spectra-cluster-cli is a command-line tool. It clusters MS/MS spectra in the [[MGF]] peak list format and writes the results to a [[.clustering]] result file. It currently supports:<br />
* Clustering of MS/MS spectra ([[MGF]] format)<br />
* Parallel processing of data<br />
<br />
== Installation ==<br />
<br />
=== Requirements ===<br />
<br />
To run the spectra-cluster-cli [https://www.oracle.com/java/index.html Java] needs to be installed on the computer.<br />
<br />
=== Downloading spectra-cluster-cli ===<br />
<br />
# Download the latest release from [https://github.com/spectra-cluster/spectra-cluster-cli/releases https://github.com/spectra-cluster/spectra-cluster-cli/releases]<br />
# Unpack the downloaded zip file. No further installation is required<br />
<br />
== Usage ==<br />
<br />
=== Preparing your data ===<br />
<br />
Peak lists must be available in [[MGF]] format. In case your data is only available in a different format, use [http://proteowizard.sourceforge.net/downloads.shtml ProteoWizard's msconvert] to convert it to [[MGF]].<br />
<br />
Optionally, identification data can be incorporated into the [[MGF]] files using the <code>SEQ=</code> tag. A tool to do this automatically is under active development and will be released shortly. The identification data does not influence the clustering process. If identification data is present in the used [[MGF]] files the corresponding data will automatically be written to the resulting [[.clustering]] files.<br />
<br />
=== Performing the clustering ===<br />
<br />
==== Summary ====<br />
<syntaxhighlight lang="bat"><br />
C:\>cd C:\Downloads\spectra-cluster-cli<br />
C:\Downloads\spectra-cluster-cli>java -jar spectra-cluster-cli-1.0-SNAPSHOT.jar -rounds 4 -threshold_end 0.99 -threshold_start 0.9999 -output_path C:\my_data\clustering_results.clustering C:\my_data\peaklists\*.mgf<br />
</syntaxhighlight><br />
<br />
==== Detailed instructions ====<br />
<br />
# Open a command prompt. On windows this is achieved by opening the <code>run</code> dialog, entering "cmd" and clicking enter (on Windows 7 simply click the windows key and immediately enter "cmd").<br />
# Navigate to the directory where you downloaded the spectra-cluster-cli tool.<br />
# Launch the spectra-cluster-cli through the command <code>java -jar spectra-cluster-cli-1.0-SNAPSHOT.jar</code> (see above). '''Note:''' the <code>spectra-cluster-cli-1.0-SNAPSHOT.jar</code> part has to be adapted based on the downloaded version.<br />
<br />
==== Additional options ====<br />
<syntaxhighlight><br />
-binary_directory <arg> path to the directory to<br />
(temporarily) store the binary<br />
files. By default a temporary<br />
directory is being created<br />
-cluster_binary_file <arg> if this option is set, only the<br />
passed binary file will be<br />
clustered and the result written<br />
to the file specified in<br />
'-output_path' in the binary<br />
format<br />
-convert_cgf if this option is set the passed<br />
CGF file is converted into a<br />
.clustering file<br />
-fast_mode if this option is set the 'fast<br />
mode' is enabled. In this mode,<br />
the radical peak filtering used<br />
for the comparison function is<br />
already applied during spectrum<br />
conversion. Thereby, the<br />
clustering and consensus spectrum<br />
quality is slightly decreased but<br />
speed increases 2-3 fold.<br />
-fragment_tolerance fragment ion tolerance in m/z to<br />
use for fragment peak matching<br />
-help print this message.<br />
-keep_binary_files if this options is set, the<br />
binary files are not deleted<br />
after clustering.<br />
-major_peak_jobs <arg> number of threads to use for<br />
major peak clustering.<br />
-merge_binary_results if this option is set, the passed<br />
binary results files are merged<br />
into a single .cgf file and<br />
written to '-output_path'<br />
-output_path <arg> path to the outputfile.<br />
Outputfile must not exist.<br />
-precursor_tolerance <arg> precursor tolerance (clustering<br />
window size) in m/z used during<br />
matching.<br />
-reuse_binary_files if this option is set, the binary<br />
files found in the binary file<br />
directory will be used for<br />
clustering.<br />
-rounds <arg> number of clustering rounds to<br />
use.<br />
-threshold_end <arg> (lowest) final clustering<br />
threshold<br />
-threshold_start <arg> (highest) starting threshold<br />
-x_learn_cdf <output filename> (Experimental option) Learn the<br />
used cumulative distribution<br />
function directly from the<br />
processed data. This is only<br />
recommended for high-resolution<br />
data. The result will be written<br />
to the defined file.<br />
-x_load_cdf <CDF filename> (Experimental option) Loads the<br />
cumulative distribution function<br />
to use from the specified file.<br />
These files can be created using<br />
the x_learn_cdf parameter<br />
-x_min_comparisons <arg> (Experimental option) Sets the<br />
minimum number of comparisons<br />
used to calculate the probability<br />
that incorrect spectra are<br />
clustered.<br />
-x_n_prefiltered_peaks <number peaks> (Experimental option) Set the<br />
number of highest peaks that are<br />
kept per spectrum during loading.<br />
</syntaxhighlight><br />
<br />
== Analysing clustering results ==<br />
<br />
We are currently working on an analysis software for clustering results in the [[.clustering]] format.</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=MSAmanda&diff=209MSAmanda2016-06-04T06:42:12Z<p>Jg: /* Running a search */</p>
<hr />
<div>{{Infobox searchengine<br />
| author = V Dorfer, P Pichler, T Stranzl, J Stadlmann, T Taus, S Winkler, K Mechtler<br />
| name = MSAmanda<br />
| citation = Dorfer et al., J Proteome Res. 2014, 13(8):3679-84<br />
| pmid = 24909410<br />
| website = http://ms.imp.ac.at/?goto=msamanda<br />
| released = 01.01.2000<br />
| operating_system = Windows, Linux, Mac OSX<br />
| input = MGF<br />
| output = text, [[mzIdentML]]<br />
| status = active<br />
| license = [http://ms.imp.ac.at/inc/pd-nodes/msamanda/LicenseAgreement_MSAmanda.rtf special license]<br />
}}<br />
<br />
MSAmanda is a free search engine developed at the [http://ms.imp.ac.at/?goto=msamanda IMP]<ref>Dorfer et al. J Proteome Res. 2014, 13(8):3679-84 [http://www.ncbi.nlm.nih.gov/pubmed/24909410 pubmed]</ref>. <br />
Most importantly it is directly integrated into ThermoFisher's ProteomeDiscoverer and SearchGUI.<br />
<br />
== Features ==<br />
<br />
MSAmanda was originally developed to replace Mascot in Karl Mechtler's lab at IMP. It is optimized to work with high-resolution data.<br />
<br />
== Supported Operating Systems ==<br />
<br />
MSAmanda is available in ProteomeDiscoverer which runs on windows. Additionally, a command line version running natively on Windows and using mono on linux and OS X is available as well.<br />
<br />
== Tutorial ==<br />
<br />
=== Installing MS Amanda ===<br />
<br />
To install MSAmanda as a stand-alone search engine.<br />
<br />
=== Running a search ===<br />
<br />
To run a search simply navigate to the folder where MSAmanda is installed<br />
<br />
<syntaxhighlight lang="bash"><br />
mono MSAmanda.exe /path/to/my/species.fasta /path/to/my/search.mgf /path/to/my/settings.xml<br />
</syntaxhighlight><br />
<br />
== References ==<br />
<references /></div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=MSAmanda&diff=208MSAmanda2016-06-04T06:41:58Z<p>Jg: /* Running a search */</p>
<hr />
<div>{{Infobox searchengine<br />
| author = V Dorfer, P Pichler, T Stranzl, J Stadlmann, T Taus, S Winkler, K Mechtler<br />
| name = MSAmanda<br />
| citation = Dorfer et al., J Proteome Res. 2014, 13(8):3679-84<br />
| pmid = 24909410<br />
| website = http://ms.imp.ac.at/?goto=msamanda<br />
| released = 01.01.2000<br />
| operating_system = Windows, Linux, Mac OSX<br />
| input = MGF<br />
| output = text, [[mzIdentML]]<br />
| status = active<br />
| license = [http://ms.imp.ac.at/inc/pd-nodes/msamanda/LicenseAgreement_MSAmanda.rtf special license]<br />
}}<br />
<br />
MSAmanda is a free search engine developed at the [http://ms.imp.ac.at/?goto=msamanda IMP]<ref>Dorfer et al. J Proteome Res. 2014, 13(8):3679-84 [http://www.ncbi.nlm.nih.gov/pubmed/24909410 pubmed]</ref>. <br />
Most importantly it is directly integrated into ThermoFisher's ProteomeDiscoverer and SearchGUI.<br />
<br />
== Features ==<br />
<br />
MSAmanda was originally developed to replace Mascot in Karl Mechtler's lab at IMP. It is optimized to work with high-resolution data.<br />
<br />
== Supported Operating Systems ==<br />
<br />
MSAmanda is available in ProteomeDiscoverer which runs on windows. Additionally, a command line version running natively on Windows and using mono on linux and OS X is available as well.<br />
<br />
== Tutorial ==<br />
<br />
=== Installing MS Amanda ===<br />
<br />
To install MSAmanda as a stand-alone search engine.<br />
<br />
=== Running a search ===<br />
<br />
To run a search simply navigate to the folder where MSAmanda is installed<br />
<br />
<syntaxhighlight lang="bash" line="0"><br />
mono MSAmanda.exe /path/to/my/species.fasta /path/to/my/search.mgf /path/to/my/settings.xml<br />
</syntaxhighlight><br />
<br />
== References ==<br />
<references /></div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=MSAmanda&diff=207MSAmanda2016-06-04T06:41:41Z<p>Jg: /* Tutorial */</p>
<hr />
<div>{{Infobox searchengine<br />
| author = V Dorfer, P Pichler, T Stranzl, J Stadlmann, T Taus, S Winkler, K Mechtler<br />
| name = MSAmanda<br />
| citation = Dorfer et al., J Proteome Res. 2014, 13(8):3679-84<br />
| pmid = 24909410<br />
| website = http://ms.imp.ac.at/?goto=msamanda<br />
| released = 01.01.2000<br />
| operating_system = Windows, Linux, Mac OSX<br />
| input = MGF<br />
| output = text, [[mzIdentML]]<br />
| status = active<br />
| license = [http://ms.imp.ac.at/inc/pd-nodes/msamanda/LicenseAgreement_MSAmanda.rtf special license]<br />
}}<br />
<br />
MSAmanda is a free search engine developed at the [http://ms.imp.ac.at/?goto=msamanda IMP]<ref>Dorfer et al. J Proteome Res. 2014, 13(8):3679-84 [http://www.ncbi.nlm.nih.gov/pubmed/24909410 pubmed]</ref>. <br />
Most importantly it is directly integrated into ThermoFisher's ProteomeDiscoverer and SearchGUI.<br />
<br />
== Features ==<br />
<br />
MSAmanda was originally developed to replace Mascot in Karl Mechtler's lab at IMP. It is optimized to work with high-resolution data.<br />
<br />
== Supported Operating Systems ==<br />
<br />
MSAmanda is available in ProteomeDiscoverer which runs on windows. Additionally, a command line version running natively on Windows and using mono on linux and OS X is available as well.<br />
<br />
== Tutorial ==<br />
<br />
=== Installing MS Amanda ===<br />
<br />
To install MSAmanda as a stand-alone search engine.<br />
<br />
=== Running a search ===<br />
<br />
To run a search simply navigate to the folder where MSAmanda is installed<br />
<br />
<syntaxhighlight lang="bash" line="1"><br />
mono MSAmanda.exe /path/to/my/species.fasta /path/to/my/search.mgf /path/to/my/settings.xml<br />
</syntaxhighlight><br />
<br />
== References ==<br />
<references /></div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Template:PMID&diff=206Template:PMID2016-06-04T06:37:10Z<p>Jg: Created page with "[https://www.ncbi.nlm.nih.gov/pubmed/{{{1}}} {{{1}}}]"</p>
<hr />
<div>[https://www.ncbi.nlm.nih.gov/pubmed/{{{1}}} {{{1}}}]</div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Template:Infobox_searchengine&diff=205Template:Infobox searchengine2016-06-04T06:36:33Z<p>Jg: Created page with "{{Infobox | bodyclass = vevent | bodystyle = {{{bodystyle|}}} | title = {{#if:{{{title|{{{name|}}}}}}|{{{title|{{{name|}}}}}}|<includeonly>{{PAGENAME}}</includeonly>}}..."</p>
<hr />
<div>{{Infobox<br />
| bodyclass = vevent<br />
| bodystyle = {{{bodystyle|}}}<br />
| title = {{#if:{{{title|{{{name|}}}}}}|{{{title|{{{name|}}}}}}|<includeonly>{{PAGENAME}}</includeonly>}}<br />
| titleclass = summary<br />
| labelstyle = white-space: nowrap;<br />
| image = {{#invoke:InfoboxImage|InfoboxImage|image={{{logo|}}}|size={{{logo size|{{{logo_size|}}}}}}|sizedefault=64px|alt={{{logo alt|{{{logo_alt|}}}}}}}}<br />
| caption = {{{logo caption|}}}<br />
| image2 = {{#if:{{{collapsible|}}}|{{hidden begin|title=Screenshot|titlestyle=text-align:center|contentstyle=text-align:center}}}}<br />
| label1 = Original author(s)<br />
| data1 = {{{author|}}}<br />
| label2 = Citation<br />
| data2 = {{{citation|}}}<br />
| label3 = PMID<br />
| data3 = {{PMID|{{{pmid}}}}}<br />
| header10 = Usage Details<br />
| label11 = Input format<br />
| data11 = {{{input|}}}<br />
| label12 = Output format<br />
| data12 = {{{output|}}}<br />
| header20 = Software Details<br />
| label21 = Website<br />
| data21 = {{#if:{{{website|}}}<br />
|{{#ifeq:{{{website|}}}|hide||{{{website|}}} }}<br />
|{{#if:{{#property:P856}}<br />
|{{URL|{{#property:P856}}}}<br />
}}<br />
}}<br />
| label22 = Operating system<br />
| data22 = {{{operating_system|}}}<br />
| label23 = [[Computing platform|Platform]]<br />
| data23 = {{{platform|}}}<br />
| label24 = License<br />
| data24 = {{{license|}}}<br />
| label25 = Initial release<br />
| data25 = {{{released|}}}<br />
| label26 = Development status<br />
| data26 = {{{status|}}}<br />
| label27 = Written in<br />
| data27 = {{{programming_language|}}}<br />
}}<noinclude><br />
{{documentation }}<br />
</noinclude></div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=MSAmanda&diff=204MSAmanda2016-06-04T06:36:10Z<p>Jg: Created page with "{{Infobox searchengine | author = V Dorfer, P Pichler, T Stranzl, J Stadlmann, T Taus, S Winkler, K Mechtler | name = MSAmanda | citation..."</p>
<hr />
<div>{{Infobox searchengine<br />
| author = V Dorfer, P Pichler, T Stranzl, J Stadlmann, T Taus, S Winkler, K Mechtler<br />
| name = MSAmanda<br />
| citation = Dorfer et al., J Proteome Res. 2014, 13(8):3679-84<br />
| pmid = 24909410<br />
| website = http://ms.imp.ac.at/?goto=msamanda<br />
| released = 01.01.2000<br />
| operating_system = Windows, Linux, Mac OSX<br />
| input = MGF<br />
| output = text, [[mzIdentML]]<br />
| status = active<br />
| license = [http://ms.imp.ac.at/inc/pd-nodes/msamanda/LicenseAgreement_MSAmanda.rtf special license]<br />
}}<br />
<br />
MSAmanda is a free search engine developed at the [http://ms.imp.ac.at/?goto=msamanda IMP]<ref>Dorfer et al. J Proteome Res. 2014, 13(8):3679-84 [http://www.ncbi.nlm.nih.gov/pubmed/24909410 pubmed]</ref>. <br />
Most importantly it is directly integrated into ThermoFisher's ProteomeDiscoverer and SearchGUI.<br />
<br />
== Features ==<br />
<br />
MSAmanda was originally developed to replace Mascot in Karl Mechtler's lab at IMP. It is optimized to work with high-resolution data.<br />
<br />
== Supported Operating Systems ==<br />
<br />
MSAmanda is available in ProteomeDiscoverer which runs on windows. Additionally, a command line version running natively on Windows and using mono on linux and OS X is available as well.<br />
<br />
== Tutorial ==<br />
<br />
=== Installing MS Amanda ===<br />
<br />
To install MSAmanda as a stand-alone search engine.<br />
<br />
== References ==<br />
<references /></div>Jghttp://wiki.proteomics-academy.org/mediawiki/index.php?title=Template:High-risk&diff=200Template:High-risk2016-06-04T06:26:43Z<p>Jg: 1 revision imported</p>
<hr />
<div>{{ombox<br />
| type = content<br />
| image = [[File:Ambox warning orange.svg|40px|alt=|link=]]<br />
| text = <br />
'''This {{<br />
#switch:{{NAMESPACE}}<br />
|Module=Lua module<br />
|#default=template<br />
}} is used on <span class="plainlinks">[https://tools.wmflabs.org/templatecount/index.php?lang=en&namespace={{NAMESPACENUMBER:{{FULLPAGENAME}}}}&name={{urlencode:{{<br />
#switch: {{SUBPAGENAME}}<br />
| doc | sandbox = {{BASEPAGENAME}}<br />
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}}}} {{#if:{{{1|}}}|{{formatnum:{{{1}}}}}|a very large number of}} pages].'''</span><br />To avoid large-scale disruption and unnecessary server load, any changes to this {{<br />
#switch:{{NAMESPACE}}<br />
|Module=module<br />
|#default=template<br />
}} should first be tested in its [[{{<br />
#switch: {{SUBPAGENAME}}<br />
| doc | sandbox = {{SUBJECTSPACE}}:{{BASEPAGENAME}}<br />
| #default = {{SUBJECTPAGENAME}}<br />
}}/sandbox|/sandbox]] or [[{{<br />
#switch: {{SUBPAGENAME}}<br />
| doc | sandbox = {{SUBJECTSPACE}}:{{BASEPAGENAME}}<br />
| #default = {{SUBJECTPAGENAME}}<br />
}}/testcases|/testcases]] subpages{{<br />
#switch:{{NAMESPACE}}<br />
|Module=.<br />
|#default=, or in your own [[Wikipedia:Subpages#How to create user subpages|user subpage]].<br />
}} The tested changes can then be added to this page in one single edit. Please consider discussing any changes on {{#if:{{{2|}}}|[[{{{2}}}]]|the [[{{<br />
#switch: {{SUBPAGENAME}}<br />
| doc | sandbox = {{TALKSPACE}}:{{BASEPAGENAME}}<br />
| #default = {{TALKPAGENAME}}<br />
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}}<noinclude><br />
{{Documentation}}<br />
<!-- Add categories to the /doc subpage; interwikis go to Wikidata, thank you! --><br />
</noinclude></div>Jg