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About Bounty Projects
This page summarizes the bounty projects available from ProteomeCommons.org. Bounty projects are modules of work that have awards associated with them. Anyone may complete the work and claim the bounty. |
Bounty Projects
Projects listed on this page are open-source bounty projects. We've got a lot of things going on here at ProteomeCommons.org, and we can't do them all at the same time. Listed on this page are project that others may complete and give to us in order to receive an associated cash bounty. Specific terms and rewards are listed with each project, but the general following rules apply unless otherwise stated.
- There is no payment for partial work, nor are you guaranteed payment if you choose to work on a project. Rewards are given once the work is validated to meet the project's requirements.
- You forfeit all rights to your work. Upon acceptance of the cash reward, you release all rights to any source-code, documentation, and other materials that you've submitted as part of the project. In all open-source projects, you will always be credited as the author of your work, but you may not reuse or resell work performed for bounty projects. We reserve the right to license bounty project work in any fashion we please.
- Once a project bounty is claimed, the project is closed and bounties will not be given for subsequent projects submitted.
- Sponsors of a project reserve the right to accept or reject a project for any reason. The stated requirements are only a best attempt at formalizing the work required.
In general, we want these projects done and we've got money to support them. If you can do the job for us, the money is yours. However, we are not promising long term work or even contract work for these bounties. We only hope to motivate developers in the ProteomeCommons.org community via cash to get particular projects done.
If you are interested in working on any of our bounty projects, please feel free to contact us directly and ask any questions you may have.
Projects
Here is the list of current bounty projects with associated rewards. Please get in touch with Jayson Falkner if you have questions about any of these projects or if you wish to claim a bounty.
Description: Fix any two formal bugs (informal bugs may count if you ask about them) from the ProteomeCommons.org IO or ProteomeCommons.org Falk Model projects.
Bounty: $50
Requirements:
- The bugs must be formally documented in the project's bug list
- You must submit the fix via a patch to the existing code
- The code must be 100% Java
T2D Specturm Reader/Writer (Completed by David Hancock)
Description: The T2D file format is a proprietary, binary file format commonly used by Applied Biosystems' instrumentation. We'd like a 100% Java driver for reading/writing this file format, and we'd like documentation of the file format. We can provide raw binary files and ASCII text versions of what we expect to be the contents of the binary file.
Bounty: $1,500
Requirements:
- The code must be 100% Java
- The code must be completely contained in the org.proteomecommons.io.t2d package.
- The reader class must properly extend org.proteomecommons.io.Reader.
- The writer class must properly extend org.proteomecommons.io.Writer.
- Plain-text documentation must be included that describes both the T2D binary format and how the T2D reader works.
- The code must be able to at least decode four given T2D files, ASCII conversions are provided for comparison. We must be able to replicate the conversion. The conversion must be generic decoding of the T2D format, and the reader must work on other similarly encoded files.
Files:
mzData Reader and Writer (Finished by Jarret Falkner 06/15/2005)
Description: The mzData file format is a relatively new, open standard for mass spec data. We'd like a 100% Java driver for reading/writing this file format, and we'd like documentation. We can provide mzXML examples and plain-text conversions.
Bounty: $250 for the readers(Finished by Jarret Falkner, 4/1/2005), $250 for the writers
Reader Requirements:
- The code must be 100% Java
- The code must be completely contained in the org.proteomecommons.io.mzdata package.
- You must implement proper extensions of the SpectrumReader, SpectrumReaderFactory, PeakListReader, and PeakListReaderFactory classes in the org.proteomecommons.io package.
- You must use a proper XML parser, and the code must be able to handle large XML files.
- Plain-text documentation must be included that describes both the mzData format and how the mzData code works.
- The code must be able to at decode some example mzData files and we must be able to replicate this functionality using other files in mzData format.
Writer Requirements:
- The code must be 100% Java
- The code must be completely contained in the org.proteomecommons.io.mzxml package.
- You must implement proper extensions of the SpectrumWriter, SpectrumWriterFactory, PeakListWriter, and PeakListWriterFactory classes in the org.proteomecommons.io package.
- Plain-text documentation must be included that describes both the mzData format and how the mzData code works.
- The code must be able to read a given mzData file in to memory and write a similar file back in to mzData format.
Documentation and example files can be found at http://psidev.sourceforge.net/ms/#mzdata.
mzXML Reader(Finished by Jarret Falkner, 3/25/2005) and Writer
Description: The mzXML file format is a relatively new, open standard for mass spec data. We'd like a 100% Java driver for reading/writing this file format, and we'd like documentation. We can provide mzXML examples and plain-text conversions.
Bounty: $250 for the readers, $250 for the writers
Reader Requirements:
- The code must be 100% Java
- The code must be completely contained in the org.proteomecommons.io.mzxml package.
- You must implement proper extensions of the SpectrumReader, SpectrumReaderFactory, PeakListReader, and PeakListReaderFactory classes in the org.proteomecommons.io package.
- You must use a proper XML parser, and the code must be able to handle large XML files.
- Plain-text documentation must be included that describes both the mzXML format and how the mzXML code works. Please reference the existing mzXML schema and documentation, don't rewrite what they've already done.
- The code must be able to at least decode the given mzXML files, ASCII conversions are provided for comparison. We must be able to replicate the conversion. The conversion must be generic decoding of the mzXML format, and the reader must work on other similarly encoded files.
- The code must be 100% Java
- The code must be completely contained in the org.proteomecommons.io.mzxml package.
- You must implement proper extensions of the SpectrumWriter, SpectrumWriterFactory, PeakListWriter, and PeakListWriterFactory classes in the org.proteomecommons.io package.
- Plain-text documentation must be included that describes both the mzXML format and how the mzXML code works. Please reference the existing mzXML schema and documentation, don't rewrite what they've already done.
- The code must be able to read the given mzXML files in to memory and write a similar file back in to mzXML format.
Files:
The file format for the ASCII conversions is in plain-text (msdat format from the Open Proteomics Database). If it is confusing, please ask for clarification.
Description: The ProteomeCommons.org IO framework currently contains a MGF reader/writer that does the bare minimum to handle parsing MSMS data in MGF format -- i.e. we can parse out precursor m/z, charge, and the peaks. We'd like the reader to handle
all the MGF meta-data and expose the meta-data in some sort of standardized fashion via the org.proteomecommons.io.mgf.MascotGenericFormatPeakListReader class. Additionally, we'd like the MGF writer to serialize the same meta-data (should it be available) in to MGF files.
Bounty: $400
Requirements:
- The reader/writer must handle all the MGF meta-data as detailed at www.matrixscience.com
- Plain-text documentation must be included that describes each piece of meta-data and how that meta-data is accessible via the PeakListReader/PeakListWriter instance
- A simple test must be included that tests the reader/writer's new functionality on at least 5 peak lists. We must be able to replicate the test results.
- The code must be 100% Java
Description: The ProteomeCommons.org IO framework currently contains a DTA reader. The DTA file format is near trivial, and the PKL format is just a bunch of DTA files grouped together, but we've yet to code proper reader/writers for each of these formats. The first person to do this gets the prize, but note this project likely won't be around for too much longer.
Bounty: $400
Requirements:
- The following four classes must be implemented: org.proteomecommons.io.dta.DTAPeakListReader, org.proteomecommons.io.dta.DTAPeakListWriter, org.proteomecommons.io.pkl.PKLPeakListReader, org.proteomecommons.io.pkl.PKLPeakListWriter. The reader classes must sub-class org.proteomecommons.io.PeakListReader and org.proteomecommons.io.PeakListWriter. The reader/writer must handle DTA/PKL data as described on www.matrixscience.com.
- Plain-text documentation must be included that describes both the DTA and PKL file formats and how the reader/writers work
- A simple test must be included that tests the reader/writer's new functionality on at least 5 peak lists. We must be able to replicate the test results.
- The code must be 100% Java
Tentative Projects
The following projects are in the queue, but they've yet to be flushed out to the point of a formal bounty project. If you are interested in any of them, please inquire and we can see about making them available.
Peptide Calculator - Completed 01/10/2005 by Jarret Falker
Description: Create a residue mass and protein digest calculator that uses the JAF framework's residue syntax and database. A user should be able to type in a peptide or protein sequence, including modified residues, and get the expected mass and pI of the peptide. Users should also be able to perform an in-silico digest, using the PeptideReader classes from the IO framework, and see the expected list of peptides. Additionally, users should be able to specify custom residues that can be registered with the JAF framework and used in appropriate calculations.
Bounty: $250
Requirements:
- The sequence syntax must comply with the stated syntax in the JAF framework.
- Users must be able to intuitively type in protein/peptide sequences and optionally digest the sequence with any of the PeptideReader classes from the ProteomeCommons.org IO framework (i.e. trypsin, non-specific, SNP).
- For each sequence analyzed an expected m/z value and pI must be provided.
- The GUI must allow for custom residues to be registered with the JAF so that they may be used in mass and pI calculations.
New Cake Theme for ProteomeCommons.org
Description: Are you artistic and do you know how to use
Blender?. We are looking to add new blender-rendered cake themes to ProteomeCommons.org. These themes will be very similar to the existing themes, but we are looking to add themes for various other types of cake such as chocolate, carrot, ice cream, and hot cakes.
Bounty: $250
Requirements:
- The 3D renderings must be done via Blender and the .blend files provided as the completed bounty.
- A complete theme must include (at least) the images described by the cake theme page.
- Creativity is encouraged, but please discuss your theme with the jfalkner@umich.edu to ensure it is suitable.
RAW Specturm Reader
Description: The RAW file format is a proprietary, binary file format commonly used by Thermo Finnigan. We'd like a 100% Java driver for reading this file format, and we'd like documentation of the file format. We can generate and provide raw binary files.
Bounty: $1,000
Requirements:
- The code must be 100% Java
- Plain-text documentation must be included that describes both the RAW binary format and how the RAW reader works.
- A simple test must be included that tests the reader's functionality on at least 5 spectra. We must be able to replicate the test results.
WIFF Specturm Reader
Description: The WIFF file format is a proprietary, binary file format commonly used by Agilent. We'd like a 100% Java driver for reading this file format, and we'd like documentation of the file format. We can generate and provide raw binary files.
Bounty: $1,000
Requirements:
- The code must be 100% Java
- Plain-text documentation must be included that describes both the WIFF binary format and how the WIFF reader works.
- A simple test must be included that tests the reader's functionality on at least 5 spectra. We must be able to replicate the test results.
GPMDB-Based Peptide Include List Generator
Description: MALDI data may be collected using several passes, possibly at much later times. Protein's that are weakly identified may be validated by going back and purposely looking for evidence the supports or disproves them. We'd like a tool that will suggest the most likely peptides for a given protein so that we can generate an include list that looks for those peptide masses.
Bounty: $500
Requirements:
- The code must be 100% Java
- Plain-text documentation must be included that describes how the code works.
- Given a protein ID, the code must look up and list all peptides for that protein that are reported in the current GPMDB.
- The user should be able to choose any of the data sources that the GPMDB offers.
- The code must also use the IO framework's TrypticPeptideReader to list all possible tryptic peptides, using an arbitrary number of missed cleaves, that fall within an arbitrary mass range (e.g. 900 through 2500 Daltons).
- The code should let users specify arbitrary modifications done to peptides (e.g. iTRAQ or carboxymethylation).
- The tool should present data to a user in two ways
- A simple GUI that for the protein lists the id/name, sequence, and size, and for each peptide lists the peptide's sequence, residue modifications, and mass.
- A plain-text file that includes just a list of the peptide's masses.
- The GUI should also lets users select which peptides should or should not have their masses in the include list. Normally we want to restrict the include lists to be only the top 4 or 5 likely peptides (i.e. whatever the GPMDB suggests and maybe one or two tryptic peptides).
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