ASMS Poster Plans (3514)

[Pratik Jagtap]

Hello Bart (and everyone),

With two months to go for ASMS Conference - it will be a good time to make plans for the ASMS poster. 

A few points that I have jotted down are (See if you want to add any more or prioritize them) :

a) Development of Galaxy-wrapped SearchGUI for MS-GF+ and Peptide Shaker.

b) Placing the above tool in toolshed.

c) Installation of the Search GUI on usegalaxyp.org

d) Testing of the tool by users and providing a feedback to developers.

e) Changes (if any) to solve bugs and go through the steps b), c) and d) again.

 f) Re-testing by users and weaving these tools into a few workflows.

We are still in step a) and will need to move on to rest so that we can test the resource.

 

Let us start a discussion so that we can have a good poster at the ASMS. 

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, Feb 7, 2014 at 11:25 PM, <sup...@on-line-registration.com> wrote:

Your abstract for the ASMS2014 was submitted on 2/8/2014. The log number for your abstract is 3514.

Community-based development and evaluation of biological mass spectrometry software via the Galaxy Tool Shed.

Bart Gottschalk2; Pratik Jagtap1; Harald Barsnes3; Marc Vaudel3; Ira Cooke4; James Johnson2; John Chilton5; Leeann Higgins1; Todd Markowski1; Trevor Wennblom2; Anne-Francoise Lamblin2; Yue Chen6; Sangtae Kim7; Lennart Martens8; Tim Griffin6

1Center for Mass Spectrometry and Proteomics, UMN, St.Paul, MN; 2Minnesota Supercomputing Institute, UMN, Minneapolis, MN; 3University of Bergen, Bergen, Norway; 4La Trobe University, Melbourne , Australia; 5PennState University, University Park, PA; 6University of Minnesota, Minneapolis, MN; 7Pacific Northwest National Laboratory, Richland, WA; 8Ghent University, Ghent, Belgium

Introduction Mass spectrometry based analysis has benefited from instrumentation and methodology advances to achieve a rapid expansion of analytic capability and application domains. But this also led to more complex analysis and an increased need for user-friendly flexible data analysis tools. Galaxy-P environment (usegalaxyp.org) enables such flexibility based on concepts of framework-ready pluggable tools and workflow assembly. Galaxy-P provides a user-oriented way for researchers to stay up to date with the latest analytical software development, while allowing developers to easily test and disseminate their tools. We present here how joint efforts by the community allow the creation of ambitious proteomics data interpretation workflows. Notably, the tools integrated in Galaxy-P are open source, user friendly and compatible with every mass spectrometer.

Methods Galaxy wrappers were developed and shared within the Galaxy Toolshed (http://toolshed.g2.bx.psu.edu) for three peptide identification algorithms: OMSSA and X!Tandem (via SearchGUI; http://searchgui.googlecode.com) and MS-GF+ (http://proteomics.ucsd.edu/Software/MSGFPlus.html). PeptideShaker was added as a versatile and powerful post-processing tool (http://peptide-shaker.googlecode.com). The tools were installed within usegalaxyp.org to create and optimize workflows around them. Parameters for running these tools and their inputs and outputs (histories) and workflows can be shared and viewed in a collaborative manner. A discussion group was created to allow users to provide feedback to developers and to exchange their experiences. The algorithms were tested on datasets acquired on variety of mass spectrometers including Orbitrap Fusion and TripleTOF 5600 instruments, allowing us to explore identification, quantification and post-translational modification (PTM) analysis applications.

Preliminary Data Using the Galaxy platform’s ability to integrate tools we integrated OMSSA and X!Tandem via the SearchGUI interface. SearchGUI was coupled to PeptideShaker providing an overview of the protein and peptide identifications along with spectral annotations, PTM analysis and a wide range of visualization, analysis and export options for any acquired dataset as well as for the reprocessing of online data (https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker). The MS-GF+ search engine was integrated in the Galaxy toolshed (http://toolshed.g2.bx.psu.edu). All three search algorithm can be applied to data from a wide-variety of instruments and experimental protocols. Moreover, being optimized for multiple processors, these algorithms are suitable for use within a high-performance computing environment. We explored the possibility of integrating it into the SearchGUI/PeptideShaker scheme as well as combining the pipeline with quantification software tools and within the existing Galaxy-P workflows for proteogenomics and metaproteomics. To test and optimize the parameters for the software tools, we used the Galaxy-P platform (usegalaxyp.org), where tools, parameters, histories and workflows can be shared between users and developers. Development and distribution of open source proteomics software will facilitate greater access to researchers in the life sciences. The Galaxy model of using a toolshed (http://toolshed.g2.bx.psu.edu) to deposit Galaxy-P framework pluggable-ready community based software creates a new paradigm in the community based development for mass spectrometry data interpretation. Well tested in genomics, it is a promising prototype for transparent, simple and wider application of advanced bioinformatic methods and their distribution among the proteomics community.

Novel Aspect Setting new paradigms in the community-based development and distribution of advanced MS proteomics data interpretation workflows via Galaxy-P.

Options: The presenting author is presenting more than one abstract. NO This material appears in another abstract from my group. NO This abstract contains commercial content. NO The presenting author is a graduate student. NO The presenting author is an undergraduate student. NO   Oral Choice: Informatics: Protein Identification Second Oral Choice: Informatics: Protein Identification Poster Choice: Informatics: Workflow and Data Management   Submitting Author:   PRATIK JAGTAP   Center for Mass Spectrometry and Proteomics, UMN   43 Gortner Laboratory   1479 Gortner Avenue   St.Paul, MN 55108   UNITED STATES     pja...@umn.edu

It is the policy of ASMS that all preliminary abstracts remain confidential by the reviewers until April 15 when all accepted abstracts officially enter the public domain. Abstracts that are not accepted remain confidential and are not published. This abstract may be edited at any time prior to the February 7 deadline.  To edit return to the abstract entry page and click Select next to the submitted abstract.

[Björn Grüning]

Hi all,

> Hello Bart (and everyone),
>
> With two months to go for ASMS Conference - it will be a good time to make
> plans for the ASMS poster.
>
> A few points that I have jotted down are (See if you want to add any more
> or prioritize them) :
>
> a) Development of Galaxy-wrapped SearchGUI for MS-GF+ and Peptide Shaker.

The developing is still happening here?
https://bitbucket.org/galaxyp/peptideshaker

I will spend some time over the weekend to drive them further.

> b) Placing the above tool in toolshed.

I would propose the test-toolshed at first. Can we use the galaxyp
account and make that a group?

> c) Installation of the Search GUI on usegalaxyp.org

I'm not sure that will be possible. usegalaxy.org is has scaling issues
and I think they will concentrate on a few NGS related fields.

> d) Testing of the tool by users and providing a feedback to developers.
> e) Changes (if any) to solve bugs and go through the steps b), c) and d)
> again.
> f) Re-testing by users and weaving these tools into a few workflows.
>
> We are still in step a) and will need to move on to rest so that we can
> test the resource.
>
> Let us start a discussion so that we can have a good poster at the ASMS.
>

Thanks Pratik for the update!
Bjoern

>
> 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, Feb 7, 2014 at 11:25 PM, <sup...@on-line-registration.com> wrote:
>
>> Your abstract for the ASMS2014 was submitted on 2/8/2014. The log number
>> for your abstract is 3514.
>>

>> *Community-based development and evaluation of biological mass
>> spectrometry software via the Galaxy Tool Shed.*
>>
>> *Bart Gottschalk*2; Pratik Jagtap1; Harald Barsnes3; Marc Vaudel3; Ira

>> Cooke4; James Johnson2; John Chilton5; Leeann Higgins1; Todd Markowski1;
>> Trevor Wennblom2; Anne-Francoise Lamblin2; Yue Chen6; Sangtae Kim7;
>> Lennart Martens8; Tim Griffin6
>>

>> *1Center for Mass Spectrometry and Proteomics, UMN, St.Paul, MN;

>> 2Minnesota Supercomputing Institute, UMN, Minneapolis, MN; 3University of
>> Bergen, Bergen, Norway; 4La Trobe University, Melbourne , Australia;
>> 5PennState University, University Park, PA; 6University of Minnesota,
>> Minneapolis, MN; 7Pacific Northwest National Laboratory, Richland, WA;

>> 8Ghent University, Ghent, Belgium*
>> *Introduction*

>> Mass spectrometry based analysis has benefited from instrumentation and
>> methodology advances to achieve a rapid expansion of analytic capability
>> and application domains. But this also led to more complex analysis and an
>> increased need for user-friendly flexible data analysis tools. Galaxy-P
>> environment (usegalaxyp.org) enables such flexibility based on concepts
>> of framework-ready pluggable tools and workflow assembly. Galaxy-P provides
>> a user-oriented way for researchers to stay up to date with the latest
>> analytical software development, while allowing developers to easily test
>> and disseminate their tools. We present here how joint efforts by the
>> community allow the creation of ambitious proteomics data interpretation
>> workflows. Notably, the tools integrated in Galaxy-P are open source, user

>> friendly and compatible with every mass spectrometer. *Methods*

>> Galaxy wrappers were developed and shared within the Galaxy Toolshed (
>> http://toolshed.g2.bx.psu.edu) for three peptide identification
>> algorithms: OMSSA and X!Tandem (via SearchGUI;
>> http://searchgui.googlecode.com) and MS-GF+ (
>> http://proteomics.ucsd.edu/Software/MSGFPlus.html). PeptideShaker was
>> added as a versatile and powerful post-processing tool (
>> http://peptide-shaker.googlecode.com). The tools were installed within
>> usegalaxyp.org to create and optimize workflows around them. Parameters
>> for running these tools and their inputs and outputs (histories) and
>> workflows can be shared and viewed in a collaborative manner. A discussion
>> group was created to allow users to provide feedback to developers and to
>> exchange their experiences. The algorithms were tested on datasets acquired
>> on variety of mass spectrometers including Orbitrap Fusion and TripleTOF
>> 5600 instruments, allowing us to explore identification, quantification and
>> post-translational modification (PTM) analysis applications.

>> *Preliminary Data*

>> among the proteomics community. *Novel Aspect*

>> Setting new paradigms in the community-based development and distribution
>> of advanced MS proteomics data interpretation workflows via Galaxy-P.

>> *Options:* The presenting author is presenting more than one abstract.
>> *NO*
>> This material appears in another abstract from my group. *NO*
>> This abstract contains commercial content. *NO*
>> The presenting author is a graduate student. *NO*
>> The presenting author is an undergraduate student. *NO*
>> *Oral Choice:* Informatics: Protein Identification *Second Oral
>> Choice:* Informatics: Protein Identification *Poster Choice:* Informatics:
>> Workflow and Data Management *Submitting Author:* PRATIK JAGTAP Center

[Pratik Jagtap]

Hello Bjoern,

Thank you for your reply. 

Regarding a) - please check with Harald and Gerben if there are any updates.

Regarding b) I will let Bart make the decision.

Regarding c) usegalaxyp.org (not usegalaxy.org)  is the public site maintained at Minnesota Supercomputing Institute for Galaxy-P with focus on proteomics applications.

Regards and Thanks,

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

[Pratik Jagtap]

Thanks Harald,

Looking forward to hearing from Gerben. It will be interesting to explore once the tool is available. 

Thanks again,

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 Wed, Apr 9, 2014 at 6:33 PM, <Harald....@biomed.uib.no> wrote:

Hi Pratik,

Regarding a) - please check with Harald and Gerben if there are any updates.

I'll forward this to Gerben. But all should be ready from the SearchGUI
and PeptideShaker side. There will be new versions out later this week
or early next week though, which also includes support for MS Amanda (for
Windows only, as this is the only platform MS Amanda is available on at
the moment). So this will make a generic SearchGUI wrapper even more
powerful. :)

Best regards,
Harald





Quoting Pratik Jagtap <pja...@umn.edu>:

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[Pratik Jagtap]

Hello Gerben,

Thanks for your mail.

Given that we have an opportunity to present this teamwork based work at the ASMS (and a possible manuscript afterwards) - will it be possible for you to coordinate with Bjoern and Ira ?

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, Apr 11, 2014 at 7:56 AM, Gerben Menschaert <gerben.m...@gmail.com> wrote:

Hi all,

We haven’t started the development of the Galaxy-wrapped new SearchGUI for X!Tandem/OMMSA/MS-GF+ (and MS Amanda).

For the moment, we’re rather preoccupied with paper submissions and also need to focus afterwards on our own ASMS presentation.  

This said, we will be starting to wrap the CLIs (tool .xml files for the 4 CLIs) next week. 

As mentioned to Harald/Marc, we definitely want to implement/maintain the SearchGUI/PeptideShaker combi for GalaxyP, 

but not necessarily within the time constrains of this ASMS poster presentation.

Kind regards,

Gerben