- galaxy-proteomics - lists.galaxyproject.org

sqlite datatype
by Jorrit Boekel 13 Feb '15

13 Feb '15

Hi JJ and mailing list, I think it was John who mailed earlier about implementing an SQLite datatype for proteomics. I sort of like this, since I find myself using SQLite all the time for my own command line tool to do filtering, protein grouping, and relating quant output to ID data. https://github.com/glormph/msstitch — I basically wrote this to combine percolator, mzidentml, and openMS intermediate formats. It’s currently a bit of a mixture of different databases and tables for different operations, but maybe it would be a good idea to have one large proteomics experiment SQLite database. Note that this is nothing I want to push onto people like it would be the next PSI standard, more like a very convenient and fast intermediate datatype. I believe that the proteome discoverer msf files are also based on sqlite. While I’m not sure if it’s a good fit for a server environment since it can get locking/access problems when accessed by too many processes, it’s a very nice fit for a bioinformatic cli tool. Are you guys currently working on any standardized SQLite thing? cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

2 1

galaxy community conference
by Jorrit Boekel 13 Feb '15

13 Feb '15

Hi all, Before I start planning my attendance, are Galaxy proteomics people going to be at the GCC in Norwich? cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

2 1

question about configuring MaxQuant and LWR on Galaxy
by Mateus Bellomo 30 Jun '14

30 Jun '14

Hi everyone, I'am trying to configure Galaxy to run MaxQuant but I'm having a little trouble. I already installed LWR and checked that it's running ok (it's running by command line and call for MaxQuant). I also confirmed that Galaxy is listenning to LWR. I've installed the package of datatypes provided by iracooke so I can upload the raw files do Galaxy. To configure the LWR I've copied some files of Galaxy-p. When I try to submit a job to the MaxQuant tool on Galaxy I get an error that I can see on the Windows terminal that is running the LWR. The error is: AttributeError : "InputsValidator" object has no attribute 'validate_configfile' I've noticed that this occurs in a python script of LWR tool. I've searched for this bug for hours without success. Any help would be appreciated. Thanks in advance

1 0

Re: [galaxy-proteomics] Worked Proteomics Example for a Galaxy Workshop?
by Ira Cooke 30 May '14

30 May '14

Many thanks Dave and Pratik, This list is a great resource. On 31 May 2014, at 6:47 am, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> wrote: Hi All, Many thanks to Pratik for sending on several new talks and posters, and details about the workshop: https://wiki.galaxyproject.org/Events/ASMS2014 or http://bit.ly/asms2014 Please let me know if there is anything else. Thanks, Dave C On Fri, May 30, 2014 at 9:17 AM, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> wrote: Hello all, If you are going to ASMS, all things Galaxy (I found 5) are listed at: https://wiki.galaxyproject.org/Events/ASMS2014 or http://bit.ly/asms2014 It prints out nicely. Feel free to take a few copies with you. Thanks, Dave C. On Thu, May 29, 2014 at 4:34 PM, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> wrote: Hi Pratik, John, and Jorrit, Thanks for all the suggestions and input. The good news is that I can wait for a new Galaxy-P 101 to be released. Perhaps fearing my complete lack of knowledge in proteomics, the workshop hosts have opted to have me cover topics that I can at least spell instead. However, long-term, it would be a wonderful thing to have a Galaxy proteomics worked example that people could use in workshops. And Jorrit, I just looked at the program for ASMS. There are several Galaxy related workshops, talks and posters this year. I'll create a wiki page listing everything, and perhaps a flyer ... I'll post to this list once that's ready. Thanks for everything, Dave C. On Thu, May 29, 2014 at 12:11 AM, Jorrit Boekel <jorrit.boekel(a)scilifelab.se<mailto:jorrit.boekel@scilifelab.se>> wrote: Hey Dave, An alternative to the problem John mentions would be to skip the RAW files altogether and start from a mzML data file downloaded from a repository (e.g. proteomexhange.org<http://proteomexhange.org/>) somewhere. To abstract your workshop from the fact that mass spec instrument manufacturers don’t provide proper accessible output formats. Hope to see many of you at ASMS in two weeks! cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 29 May 2014, at 00:20, John Chilton <jmchilton(a)gmail.com<mailto:jmchilton@gmail.com>> wrote: > Hey Dave, > > Yeah the example is pretty old and it seems the Galaxy-P team no > longer distributes a Galaxy-P specific code base - but *in theory* one > should be able to get most of the needed tools from the tool shed. If > you attempt this tutorial on a fresh instance of Galaxy you are not > going to be able to do the very first step though - extracting raw > files. This requires a Windows server for Galaxy to communicate with > the LWR or a customized WINE emulation environment. Perhaps you can do > the first step on the public Galaxy-P server and just take the > resulting file and do your analysis from there on? Good luck :). > > -John > > > On Sat, May 24, 2014 at 7:33 AM, Pratik Jagtap <pjagtap(a)umn.edu<mailto:pjagtap@umn.edu>> wrote: >> Hello Dave, >> >> Thanks for the mail. >> >> The Galaxy-P 101 was written and used by us (John Chilton and myself) in >> November 2012 and it was last tested in July 2013. It will be great if >> anyone has an opportunity to see if and how it works. >> >> There is a need for a new GalaxyP 101 - which we will do so after we have >> new set of tools such as MS-GF+ and PeptideShaker installed. As we publish, >> we will also have pages and tutorials for proteogenomics and metaproteomics >> workflows. >> >>> Galaxy-P folks: How do you feel about others using the Galaxy-P 101 in > >>> workshops? I can imagine installing all the tools on the workshop servers > >>> (in which case it seems like an easy win), or running directly off Galaxy-P >>> (which would better highlight Galaxy-P, but put a load on your servers). >> >> Once tested, I think it is a good idea to have GalaxyP101 on the workshop >> servers. >> >> For most of our proteomics work - we have been using ProteinPilot ( a >> Windows-based commercial tool). We have a webinar available in case users >> are interested - z.umn.edu/ppingp<http://z.umn.edu/ppingp> >> >> Thanks and Regards, >> >> Pratik >> >> Pratik Jagtap, >> Managing Director, >> Center for Mass Spectrometry and Proteomics, >> 43 Gortner Laboratory >> 1479 Gortner Avenue >> St. Paul, MN 55108 >> Phone: 612-624-9275 >> >> >> On Fri, May 23, 2014 at 11:54 AM, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> >> wrote: >>> >>> Hi Pratik and JJ, >>> >>> Just a heads up that there's a relevant thread on the Galaxy-Proteomics >>> list that you might want to respond to. >>> >>> Bart is on the list, but I don't think either of you are. If you respond, >>> please respond on-list, if you are comfortable with that. >>> >>> Thanks, >>> >>> Dave C >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> >>> Date: Fri, May 23, 2014 at 9:52 AM >>> Subject: Re: [galaxy-proteomics] Worked Proteomics Example for a Galaxy >>> Workshop? >>> To: Ira Cooke <I.Cooke(a)latrobe.edu.au<mailto:I.Cooke@latrobe.edu.au>> >>> Cc: Galaxy Proteomics List <galaxy-proteomics(a)lists.bx.psu.edu<mailto:galaxy-proteomics@lists.bx.psu.edu>> >>> >>> >>> Hi Ira, >>> >>> Thanks for the pointer. And many thanks to the Galaxy-P folks for >>> creating this. In hindsight (which I'm really good at), Galaxy-P seems an >>> obvious place to look for this. >>> >>> The example looks enormous, but it's well documented. I'll give it a >>> careful look. >>> >>> And, for this workshop and for future reference: >>> >>> Galaxy-P folks: How do you feel about others using the Galaxy-P 101 in >>> workshops? I can imagine installing all the tools on the workshop servers >>> (in which case it seems like an easy win), or running directly off Galaxy-P >>> (which would better highlight Galaxy-P, but put a load on your servers). >>> >>> Thanks again, >>> >>> Dave C. >>> >>> >>> >>> >>> On Thu, May 22, 2014 at 5:36 PM, Ira Cooke <I.Cooke(a)latrobe.edu.au<mailto:I.Cooke@latrobe.edu.au>> wrote: >>>> >>>> Hi Dave, >>>> >>>> I haven’t gone through it myself, but this looks good >>>> >>>> https://usegalaxyp.readthedocs.org/en/latest/sections/galaxyp_101.html >>>> >>>> Cheers >>>> Ira >>>> >>>> >>>> On 23 May 2014, at 5:11 am, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> >>>> wrote: >>>> >>>> Hello all, >>>> >>>> Does anyone know of worked proteomics analysis that I could use for a >>>> Galaxy workshop? I'm giving a workshop in July and the hosts are interested >>>> in proteomics. I did tell them I currently have no knowledge of proteomics, >>>> so they aren't expecting me to cover it. However, if a ready made example >>>> is out there, I might be able to come up to speed on the basics before then >>>> >>>> Thanks, >>>> >>>> Dave C >>>> >>>> -- >>>> http://galaxyproject.org/GCC2014 >>>> http://galaxyproject.org/ >>>> http://getgalaxy.org/ >>>> http://usegalaxy.org/ >>>> https://wiki.galaxyproject.org/ >>>> _______________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> http://lists.bx.psu.edu/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >>>> >>> >>> >>> >>> -- >>> http://galaxyproject.org/GCC2014 >>> http://galaxyproject.org/ >>> http://getgalaxy.org/ >>> http://usegalaxy.org/ >>> https://wiki.galaxyproject.org/ >>> >>> >>> >>> -- >>> http://galaxyproject.org/GCC2014 >>> http://galaxyproject.org/ >>> http://getgalaxy.org/ >>> http://usegalaxy.org/ >>> https://wiki.galaxyproject.org/ >> >> >> >> _______________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > _______________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ _______________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ _______________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

1 0

Re: [galaxy-proteomics] Worked Proteomics Example for a Galaxy Workshop?
by Pratik Jagtap 30 May '14

30 May '14

Hello Dave, Thanks for the mail. The Galaxy-P 101<https://usegalaxyp.readthedocs.org/en/latest/sections/galaxyp_101.html> was written and used by us (John Chilton and myself) in November 2012 and it was last tested in July 2013. It will be great if anyone has an opportunity to see if and how it works. There is a need for a new GalaxyP 101 - which we will do so after we have new set of tools such as MS-GF+ and PeptideShaker installed. As we publish, we will also have pages and tutorials for proteogenomics and metaproteomics workflows. *> Galaxy-P folks*: How do you feel about others using the Galaxy-P 101 in > workshops? I can imagine installing all the tools on the workshop servers > (in which case it seems like an easy win), or running directly off Galaxy-P (which would better highlight Galaxy-P, but put a load on your servers). Once tested, I think it is a good idea to have GalaxyP101 on the workshop servers. For most of our proteomics work - we have been using ProteinPilot ( a Windows-based commercial tool). We have a webinar available in case users are interested - z.umn.edu/ppingp Thanks and Regards, Pratik Pratik Jagtap, Managing Director, Center for Mass Spectrometry and Proteomics, 43 Gortner Laboratory 1479 Gortner Avenue St. Paul, MN 55108 Phone: 612-624-9275 On Fri, May 23, 2014 at 11:54 AM, Dave Clements <clements(a)galaxyproject.org>wrote: > Hi Pratik and JJ, > > Just a heads up that there's a relevant thread on the Galaxy-Proteomics > list that you might want to respond to. > > Bart is on the list, but I don't think either of you are. If you respond, > please respond on-list, if you are comfortable with that. > > Thanks, > > Dave C > > > > ---------- Forwarded message ---------- > From: Dave Clements <clements(a)galaxyproject.org> > Date: Fri, May 23, 2014 at 9:52 AM > Subject: Re: [galaxy-proteomics] Worked Proteomics Example for a Galaxy > Workshop? > To: Ira Cooke <I.Cooke(a)latrobe.edu.au> > Cc: Galaxy Proteomics List <galaxy-proteomics(a)lists.bx.psu.edu> > > > Hi Ira, > > Thanks for the pointer. And many thanks to the Galaxy-P folks for > creating this. In hindsight (which I'm *really* good at), Galaxy-P seems > an obvious place to look for this. > > The example looks enormous, but it's well documented. I'll give it a > careful look. > > And, for this workshop and for future reference: > > *Galaxy-P folks*: How do you feel about others using the Galaxy-P 101 in > workshops? I can imagine installing all the tools on the workshop servers > (in which case it seems like an easy win), or running directly off Galaxy-P > (which would better highlight Galaxy-P, but put a load on your servers). > > Thanks again, > > Dave C. > > > > > On Thu, May 22, 2014 at 5:36 PM, Ira Cooke <I.Cooke(a)latrobe.edu.au> wrote: > >> Hi Dave, >> >> I haven’t gone through it myself, but this looks good >> >> https://usegalaxyp.readthedocs.org/en/latest/sections/galaxyp_101.html >> >> Cheers >> Ira >> >> >> On 23 May 2014, at 5:11 am, Dave Clements <clements(a)galaxyproject.org> >> wrote: >> >> Hello all, >> >> Does anyone know of worked proteomics analysis that I could use for a >> Galaxy workshop? I'm giving a workshop in July and the hosts are >> interested in proteomics. I did tell them I currently have no knowledge of >> proteomics, so they aren't expecting me to cover it. However, if a ready >> made example is out there, I might be able to come up to speed on the >> basics before then >> >> Thanks, >> >> Dave C >> >> -- >> http://galaxyproject.org/GCC2014 >> http://galaxyproject.org/ >> http://getgalaxy.org/ >> http://usegalaxy.org/ >> https://wiki.galaxyproject.org/ >> _______________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> >> >> > > > -- > http://galaxyproject.org/GCC2014 > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > https://wiki.galaxyproject.org/ > > > > -- > http://galaxyproject.org/GCC2014 > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > https://wiki.galaxyproject.org/ >

4 5

Re: [galaxy-proteomics] Worked Proteomics Example for a Galaxy Workshop?
by Ira Cooke 23 May '14

23 May '14

Hi Dave, I haven’t gone through it myself, but this looks good https://usegalaxyp.readthedocs.org/en/latest/sections/galaxyp_101.html Cheers Ira On 23 May 2014, at 5:11 am, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> wrote: Hello all, Does anyone know of worked proteomics analysis that I could use for a Galaxy workshop? I'm giving a workshop in July and the hosts are interested in proteomics. I did tell them I currently have no knowledge of proteomics, so they aren't expecting me to cover it. However, if a ready made example is out there, I might be able to come up to speed on the basics before then Thanks, Dave C -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ _______________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

2 1

Move to Google Groups
by Dave Clements 22 May '14

22 May '14

Hello Galaxy Proteomicists! The Galaxy Project has started to create new mailing lists using a Google Groups infrastructure. The new lists still work like mailing lists (plus other stuff). We are hoping that Google Groups proves to be less maintenance than Mailman. We are also considering moving our established lists to Google too. Since this is the smallest and least active of the Galaxy community's mailing lists, this is the first established list we are going to move. Look for this to happen before GCC2014. If anyone has any requests or questions about the move, please let us know. Thanks, Dave C PS: John Chilton originally wanted this list set up on Google Groups. I talked him out of it. There can't possibly be a lesson for me in that experience, can there? ;-) -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0

Worked Proteomics Example for a Galaxy Workshop?
by Dave Clements 22 May '14

22 May '14

Hello all, Does anyone know of worked proteomics analysis that I could use for a Galaxy workshop? I'm giving a workshop in July and the hosts are interested in proteomics. I did tell them I currently have no knowledge of proteomics, so they aren't expecting me to cover it. However, if a ready made example is out there, I might be able to come up to speed on the basics before then Thanks, Dave C -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0

Fwd: [bioinfo] Post-doctoral position in computational mass spectrometry at CEA Saclay (France, Paris area)
by Dave Clements 15 Apr '14

15 Apr '14

Hello all, Forwarding this from SFBI list. Dave C ---------- Forwarded message ---------- From: <etienne.thevenot(a)cea.fr> Date: Tue, Apr 15, 2014 at 1:07 AM Subject: [bioinfo] Post-doctoral position in computational mass spectrometry at CEA Saclay (France, Paris area) To: bioinfo(a)sfbi.fr Innovative algorithms and software tools for spectra interpretation and structure elucidation in metabolomics Background The Laboratory for Data Analysis and Smart Systems (LADIS) at CEA (French Alternative Energies and Atomic Energy Commission) has strong expertise in processing and analysis of mass spectrometry (MS) data and has a longstanding partnership with Laboratory of Drug Metabolism (LEMM) which is specialized in LC-MS metabolomics. Together with three INRA platforms (PFEM, BMP and MetaToul at Clermont-Ferrand, Bordeaux and Toulouse, respectively), we develop the bioinformatics tools for MetaboHUB, the national infrastructure in metabolomics and fluxomics (www.metabohub.fr/en) The three main tasks are: 1) developing a Galaxy workflow for data processing, analysis and annotation (in collaboration with the French Institute for Bioinformatics), 2) building a reference database for compounds and spectra (NMR and MS) with the corresponding tools for spectra visualization, matching and interpretation, and 3) managing the data and metadata resulting from the analysis of samples from large cohorts on the four platforms. As metabolomics is increasingly used for biomarker discovery, high-throughput annotation of MS peak signals is critical. Within task 2, the development of efficient algorithms for mass spectra interpretation is tightly coupled to the building of a comprehensive database of high quality spectra. Whereas software tools exist for the determination of the chemical formula (based on mass accuracy, analysis of isotope distribution, etc.), the elucidation of de novo structures (i.e. from unknown compounds) through interpretation of fragmentation spectra (MS/MS) remains challenging due to the chemical diversity of metabolites. Such a task requires the ability to develop efficient combinatorial algorithms and interactive visualization tools in addition to a good knowledge of both the rules of ionization and fragmentation in the gas phase. Project Within the MetaboHUB project, the post holder will develop the software tools to interpret MS/MS spectra and determine the structure of previously uncharacterized compounds. He/she will work with Pr. Jean-Claude Tabet to automate the process of spectrum interpretation by 1) determining the metadata regarding spectrum acquisition to be stored in the database, 2) designing and implementing the algorithms for MS and MS/MS spectra matching, chemical structure elucidation and visualization, and 3) integrating the tools in the MetaboHUB database. In addition, the post holder will contribute to task 3 by benchmarking software tools and architecture solutions for collaborative management of the huge amount of raw and processed data generated simultaneously by the four MetaboHUB platforms. Profile The successful candidate should hold a PhD in cheminformatics, bioinformatics or computer science and have a strong understanding of organic chemistry. The candidate is expected to have experience with Java and C++, with database management systems (MySQL) and with web content management systems (jQuery). The candidate should have presented his/her Ph.D. thesis for less than two years before the starting date and should have a good record of scientific publications. Our offer 1-year contract (renewable once). Net salary: about 2200 €/month, depending on experience. Application Please send your CV and your letter of motivation to: Etienne Thévenot Laboratory for Data Analysis and Smart Systems CEA, Saclay Center, build. 565 (DRT/LIST/DM2I/LADIS) F-91191 Gif-sur-Yvette Cedex, France Mail: etienne.thevenot(a)cea.fr Website: http://www-centre-saclay.cea.fr/en -- http://www.sfbi.fr Archives : http://listes.sfbi.fr/wws/arc/bioinfo -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0

ASMS Abstract Deadline is February 7
by Dave Clements 22 Jan '14

22 Jan '14

Hello all, Last year there was an enormous Galaxy presence at the ASMS conference: https://wiki.galaxyproject.org/Events/ASMS2013 I have no idea if there will be another swarming presence in 2014, but if you are planning to present something then please let me know and I'll do my best to let the world know about it. The abstract deadline is February 7. See http://www.asms.org/conferences/annual-conference/abstract-submission. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0