Galaxy for Proteomics

1–24 of 24

This is a google group for users and developers of Galaxy-P resource. Currently, we are testing the integration of MS-GF+, X! tandem, OMSSA and PeptideShaker into Galaxy-P.

Developers will use the galaxy toolshed to install Galaxy-environment compatible software tools. (http://z.umn.edu/galaxytoolshedproteomics)
Developers at MSI will install these tools onto usegalaxyp.org
Users will test the tool and provide feedback on these tools.

0 selected

Björn Grüning

11/12/18

systematic and regular workflow testing

Hi GalaxyP, usegalaxy.eu has started to enable regular workflow testing and I was able to get the

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systematic and regular workflow testing

Hi GalaxyP, usegalaxy.eu has started to enable regular workflow testing and I was able to get the

11/12/18

Björn Grüning

4/28/17

Training material

Hi, just a heads up. We fixed a little bit the training material. Now the metadata is at least

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Training material

Hi, just a heads up. We fixed a little bit the training material. Now the metadata is at least

4/28/17

Pratik Jagtap, … Marc Vaudel41

12/9/15

Re: New Version of Peptideshaker

Hi Gerben, The changes are essentially on Comet itself, and our parsing of ms-gf+. These changes only

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Re: New Version of Peptideshaker

Hi Gerben, The changes are essentially on Comet itself, and our parsing of ms-gf+. These changes only

12/9/15

Pratik Jagtap, … Marc Vaudel5

8/11/15

mzml inputs for SearchGUI?

Hello Marc and Bjoern, Thanks for the inputs. Locally, we do use the Galaxy-wrapped msconvert to

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mzml inputs for SearchGUI?

Hello Marc and Bjoern, Thanks for the inputs. Locally, we do use the Galaxy-wrapped msconvert to

8/11/15

Pratik Jagtap, … Tim Griffin7

4/28/15

SearchGUI / PeptideShaker testing within GalaxyP (April 2015 tests).

Thanks for the comments Ira. I'll put a couple of comments on top of yours: 1. As these issues

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SearchGUI / PeptideShaker testing within GalaxyP (April 2015 tests).

Thanks for the comments Ira. I'll put a couple of comments on top of yours: 1. As these issues

4/28/15

Pratik Jagtap, … Björn Grüning52

2/19/15

Galaxy wrapping of SearchGUI-1.23.3 and PeptideShaker-0.35.6

Thanks Bjoern, We can test the latest GUI versions and see how they work for small datasets. However,

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Galaxy wrapping of SearchGUI-1.23.3 and PeptideShaker-0.35.6

Thanks Bjoern, We can test the latest GUI versions and see how they work for small datasets. However,

2/19/15

Pratik Jagtap, Ira Cooke6

2/16/15

Fwd: Development tracking, communication and high-level summary for OpenSWATH.

Hello Everyone, Here is a Wiki that we will use to track and document the progress. https://github.

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Fwd: Development tracking, communication and high-level summary for OpenSWATH.

Hello Everyone, Here is a Wiki that we will use to track and document the progress. https://github.

2/16/15

Pratik Jagtap, … Marc Vaudel7

2/10/15

Can PeptideShaker outputs be used for OpenSWATH analysis?

> I'm currently away on leave and don't have easy access to an example peptideshaker mzid

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Can PeptideShaker outputs be used for OpenSWATH analysis?

> I'm currently away on leave and don't have easy access to an example peptideshaker mzid

2/10/15

Candace Guerrero, … Marc Vaudel3

11/26/14

Hi Candace, As Harald mentioned and as detailed in an earlier mail, we designed the zip export so

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Hi Candace, As Harald mentioned and as detailed in an earlier mail, we designed the zip export so

11/26/14

Pratik Jagtap, … harald.barsnes27

11/25/14

Testing of SearchGUI-1.23.0 and PeptideShaker-0.35.2 (outside GalaxyP)

Hi Pratik, It would again seem like you have problems with the connection to the database dropping in

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Testing of SearchGUI-1.23.0 and PeptideShaker-0.35.2 (outside GalaxyP)

Hi Pratik, It would again seem like you have problems with the connection to the database dropping in

11/25/14

Pratik Jagtap, … Björn Grüning15

11/17/14

A tool that parses out proteomic databases from UniProt with species as an input?

Hi, >> For msconvert, we do use a LWR (or Pulsar) to convert RAW files into mzml > (or MGF).

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A tool that parses out proteomic databases from UniProt with species as an input?

Hi, >> For msconvert, we do use a LWR (or Pulsar) to convert RAW files into mzml > (or MGF).

11/17/14

Pratik Jagtap, Marc Vaudel5

11/17/14

SearchGUI and PeptideShaker for large database search.

Hi Pratik, Thank you for the information, that looks very promising. If you are using PSM level

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SearchGUI and PeptideShaker for large database search.

Hi Pratik, Thank you for the information, that looks very promising. If you are using PSM level

11/17/14

Ebbing de Jong, … Pratik Jagtap5

10/24/14

Fwd: [MSI #67787] AutoReply: addition of features in Galaxy-P (proteases)

Hello Bjoern, We are requesting one of our MSI developers to make changes and install the software.

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Fwd: [MSI #67787] AutoReply: addition of features in Galaxy-P (proteases)

Hello Bjoern, We are requesting one of our MSI developers to make changes and install the software.

10/24/14

10/24/14

Wrapping latest version of PeptideShaker for GalaxyP.

Hello Ira and Bjoern, I am copying JJ and Bart on this so that they are on the same page / can

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Wrapping latest version of PeptideShaker for GalaxyP.

Hello Ira and Bjoern, I am copying JJ and Bart on this so that they are on the same page / can

10/24/14

Candace Guerrero, … Ira Cooke15

10/24/14

iracooke@gmail.com, bjoern.gruening@gmail.com, marc.vaudel@biomed.uib.no, harald.barsnes@gmail.com

Hi Bjoern, Great to hear from you. My preference would be to keep this as a separate repository as

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iracooke@gmail.com, bjoern.gruening@gmail.com, marc.vaudel@biomed.uib.no, harald.barsnes@gmail.com

Hi Bjoern, Great to hear from you. My preference would be to keep this as a separate repository as

10/24/14

Pratik Jagtap, … Björn Grüning15

9/11/14

First tests with PeptideShaker.

Sure, will do ... the idea is to generate them automatically ... we will so how successful we are :)

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First tests with PeptideShaker.

Sure, will do ... the idea is to generate them automatically ... we will so how successful we are :)

9/11/14

6/25/14

Re: PeptideShaker/SearchGui on the toolshed

Thanks Ira, As discussed yesterday, we will request developers at MSI to install this on the

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Re: PeptideShaker/SearchGui on the toolshed

Thanks Ira, As discussed yesterday, we will request developers at MSI to install this on the

6/25/14

Pratik Jagtap, … Björn Grüning9

6/20/14

Initial testing on PeptideShaker within Galaxy environment.

Details of testing after Ira's visit to Minneapolis. - Pratik ---------- Forwarded message ------

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Initial testing on PeptideShaker within Galaxy environment.

Details of testing after Ira's visit to Minneapolis. - Pratik ---------- Forwarded message ------

6/20/14

Pratik Jagtap, … Björn Grüning26

5/20/14

Re: MS-GF+ added to SearchGUI and PeptideShaker

Hello Bjoern, > @Pratik, are there any news from the testing unit :) ? I will test it as soon as

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Re: MS-GF+ added to SearchGUI and PeptideShaker

Hello Bjoern, > @Pratik, are there any news from the testing unit :) ? I will test it as soon as

5/20/14

Pratik Jagtap, Björn Grüning5

4/11/14

ASMS Poster Plans (3514)

Hello Gerben, Thanks for your mail. Given that we have an opportunity to present this teamwork based

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ASMS Poster Plans (3514)

Hello Gerben, Thanks for your mail. Given that we have an opportunity to present this teamwork based

4/11/14

3/19/14

Re: First steps for MS-GF+ and PeptideShaker integration within Galaxy-P.

Thanks Harald, This is great progress - thanks so much ! I spoke with Ira recently - and he (along

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Re: First steps for MS-GF+ and PeptideShaker integration within Galaxy-P.

Thanks Harald, This is great progress - thanks so much ! I spoke with Ira recently - and he (along

3/19/14

3/7/14

Fwd: [galaxy-iuc] Required Tool Dependencies and new packages

Communication with Ira and Bjoern. - Pratik ---------- Forwarded message ---------- From: Pratik

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Fwd: [galaxy-iuc] Required Tool Dependencies and new packages

Communication with Ira and Bjoern. - Pratik ---------- Forwarded message ---------- From: Pratik

3/7/14

2/14/14

MS-GF+ Wrapper.

Just ensuring that Lennart, Marc and Harald got this message. Regards, Pratik On Friday, February 14,

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MS-GF+ Wrapper.

Just ensuring that Lennart, Marc and Harald got this message. Regards, Pratik On Friday, February 14,

irac...@gmail.com

2/14/14

2/14/14

Hello Lennart, Marc, Harald, Ira, Bart and Tim, Welcome to the google group that we will use for

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Hello Lennart, Marc, Harald, Ira, Bart and Tim, Welcome to the google group that we will use for

2/14/14

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