May 2014 - galaxy-proteomics - lists.galaxyproject.org

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/

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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/ >

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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/

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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/

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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/

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