Microsoft Computational Biology Tools

UPDATED WIKI: Hla Completion

CarlK — Mon, 17 Dec 2007 19:43:47 GMT

HLA Completion

NEWS: 12/17/2007 - A new version of HLA Completion is in the works

Web Version, including general information

http://atom.research.microsoft.com/bio/hlacomp.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Linkdis\Linkdis.sln
Build directory: Linkdis\HlaCompletion\bin\Release

Exe

HlaCompletion.exe

How to run regression tests

UPDATED WIKI: PhyloD

CarlK — Thu, 15 Nov 2007 19:17:28 GMT

PhyloD

References

Z. Brumme, C. Brumme, D. Heckerman, B. Korber, M. Daniels, J. Carlson, C. Kadie, T. Bhattacharya, C. Chui, T. Mo, R. Hogg, J. Montaner, N. Frahm, C. Brander, B. Walker, P. Harrigan. Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1. PLoS Pathogens, 3(7): e94, July 2007.

J. Carlson, C. Kadie, S. Mallal, and D. Heckerman. Leveraging hierarchical population structure in discrete association studies. PLoS ONE, 2(7): e591, July 2007.

Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie,Jonathan Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber. Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations. Science 16 March 2007: Vol. 315. no. 5818, pp. 1583 - 1586

Web Version, including some general information

http://atom.research.microsoft.com/bio/phylod.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: PhyloTree\PhyloTree.sln
Build directory: PhyloTree\PhyloD\bin\Release
Build directory: PhyloTree\Tabulate\bin\Release

Solution file: PhyloTree\PhyloDCCS.sln
Build directory: PhyloTree\PhyloDCcs\bin\Release

Solution file: PhyloTree\PhyloDDNsln
Build directory: PhyloTree\PhyloDDN\bin\Release

Exe's:

PhyloD.exe

Regression Test: PhyloTree\PhyloD\RegressionTest

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

PhyloDCcs.exe
PhyloDDN.exe

Regression Test: PhyloTree\PhyloDDN\RegressionTest

How to run regression tests

UPDATED WIKI: HLA Assignment

CarlK — Thu, 15 Nov 2007 19:15:18 GMT

HLA Assignment

References

J. Listgarten,N. Frahm, C. Kadie, C. Brander, D. Heckerman. A statistical framework for modeling HLA-dependent T cell response data, PLoS Computational Biology, 3(10): e188, October 2007.

N. Frahm, K. Yusim, T. Suscovich, S. Adams, J. Sidney, P. Hraber, H. Hewitt, Ca. Linde, D. Kavanagh, T. Woodberry, L. Henry, K. Faircloth, J. Listgarten,C. Kadie,N. Jojic,K. Sango, N. Brown, E. Pae, M. Zaman, F. Bihl, A. Khatri, M. John, S. Mallal, F. Marincola, B. Walker, A. Sette, D. Heckerman,B. Korber, C. Brander. Extensive HLA class I allele promiscuity among viral CTL epitopes. European Journal of Immunology, 37, August 2007.

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: HLA Assignment

heckerma — Thu, 15 Nov 2007 17:25:25 GMT

HLA Assignment

References

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: HLA Assignment

heckerma — Thu, 15 Nov 2007 17:24:31 GMT

HLA Assignment

References

J. Listgarten,N. Frahm, C. Kadie,C. Brander, D. Heckermanhttp://research.microsoft.com/~heckerman/. A statistical framework for modeling HLA-dependent T cell response data, PLoS Computational Biology, 3(10): e188, October 2007.

N. Frahm, K. Yusim, T. Suscovich, S. Adams, J. Sidney, P. Hraber, H. Hewitt, Ca. Linde, D. Kavanagh, T. Woodberry, L. Henry, K. Faircloth, J. Listgarten,C. Kadie,N. Jojic,K. Sango, N. Brown, E. Pae, M. Zaman, F. Bihl, A. Khatri, M. John, S. Mallal, F. Marincola, B. Walker, A. Sette, D. Heckerman,B. Korber, C. Brander. Extensive HLA class I allele promiscuity among viral CTL epitopes. European Journal of Immunology, 37, August 2007.

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: PhyloD

heckerma — Thu, 15 Nov 2007 17:23:35 GMT

PhyloD

References

Z. Brumme, C. Brumme, D. Heckerman, B. Korber, M. Daniels, J. Carlson, C. Kadie,T. Bhattacharya, C. Chui, T. Mo, R. Hogg, J. Montaner, N. Frahm, C. Brander, B. Walker, P. Harrigan. Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1. PLoS Pathogens, 3(7): e94, July 2007.

J. Carlson, C. Kadie, S. Mallal, and D. Heckerman. Leveraging hierarchical population structure in discrete association studies. PLoS ONE, 2(7): e591, July 2007.

Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie,Jonathan Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber. Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations. Science 16 March 2007: Vol. 315. no. 5818, pp. 1583 - 1586

Web Version, including some general information

http://atom.research.microsoft.com/bio/phylod.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: PhyloTree\PhyloTree.sln
Build directory: PhyloTree\PhyloD\bin\Release
Build directory: PhyloTree\Tabulate\bin\Release

Solution file: PhyloTree\PhyloDCCS.sln
Build directory: PhyloTree\PhyloDCcs\bin\Release

Solution file: PhyloTree\PhyloDDNsln
Build directory: PhyloTree\PhyloDDN\bin\Release

Exe's:

PhyloD.exe

Regression Test: PhyloTree\PhyloD\RegressionTest

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

PhyloDCcs.exe
PhyloDDN.exe

Regression Test: PhyloTree\PhyloDDN\RegressionTest

How to run regression tests

UPDATED WIKI: PhyloD

heckerma — Thu, 15 Nov 2007 17:23:13 GMT

PhyloD

References

Z. Brumme, C. Brumme, D. Heckerman, B. Korber, M. Daniels, J. Carlson, C. Kadie,T. Bhattacharya, C. Chui, T. Mo, R. Hogg, J. Montaner, N. Frahm, C. Brander, B. Walker, P. Harrigan. Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1. PLoS Pathogens, 3(7): e94, July 2007.

J. Carlson, C. Kadie,S. Mallal, and D. Heckerman. Leveraging hierarchical population structure in discrete association studies. PLoS ONE, 2(7): e591, July 2007.

Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie,Jonathan Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber. Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations. Science 16 March 2007: Vol. 315. no. 5818, pp. 1583 - 1586

Web Version, including some general information

http://atom.research.microsoft.com/bio/phylod.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: PhyloTree\PhyloTree.sln
Build directory: PhyloTree\PhyloD\bin\Release
Build directory: PhyloTree\Tabulate\bin\Release

Solution file: PhyloTree\PhyloDCCS.sln
Build directory: PhyloTree\PhyloDCcs\bin\Release

Solution file: PhyloTree\PhyloDDNsln
Build directory: PhyloTree\PhyloDDN\bin\Release

Exe's:

PhyloD.exe

Regression Test: PhyloTree\PhyloD\RegressionTest

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

PhyloDCcs.exe
PhyloDDN.exe

Regression Test: PhyloTree\PhyloDDN\RegressionTest

How to run regression tests

UPDATED WIKI: HLA Assignment

heckerma — Thu, 15 Nov 2007 17:21:41 GMT

HLA Assignment

References

J. Listgarten,N. Frahm, C. Kadie,C. Brander, D. Heckerman. http://research.microsoft.com/~heckerman/A statistical framework for modeling HLA-dependent T cell response data, PLoS Computational Biology, 3(10): e188, October 2007.

N. Frahm, K. Yusim, T. Suscovich, S. Adams, J. Sidney, P. Hraber, H. Hewitt, Ca. Linde, D. Kavanagh, T. Woodberry, L. Henry, K. Faircloth, J. Listgarten,C. Kadie,N. Jojic,K. Sango, N. Brown, E. Pae, M. Zaman, F. Bihl, A. Khatri, M. John, S. Mallal, F. Marincola, B. Walker, A. Sette, D. Heckerman,B. Korber, C. Brander. Extensive HLA class I allele promiscuity among viral CTL epitopes. European Journal of Immunology, 37, August 2007.

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: HLA Assignment

heckerma — Thu, 15 Nov 2007 17:20:59 GMT

HLA Assignment

References

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: HLA Assignment

heckerma — Thu, 15 Nov 2007 17:20:22 GMT

HLA Assignment

References

J. Listgarten,N. Frahm, C. Kadie,C. Brander, D. Heckerman.http://research.microsoft.com/~heckerman/A statistical framework for modeling HLA-dependent T cell response data, PLoS Computational Biology, 3(10): e188, October 2007.

N. Frahm, K. Yusim, T. Suscovich, S. Adams, J. Sidney, P. Hraber, H. Hewitt, Ca. Linde, D. Kavanagh, T. Woodberry, L. Henry, K. Faircloth, J. Listgarten,C. Kadie,N. Jojic,K. Sango, N. Brown, E. Pae, M. Zaman, F. Bihl, A. Khatri, M. John, S. Mallal, F. Marincola, B. Walker, A. Sette, D. Heckerman,B. Korber, C. Brander. Extensive HLA class I allele promiscuity among viral CTL epitopes.European Journal of Immunology, 37, August 2007.

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: PhyloD

CarlK — Thu, 15 Nov 2007 16:46:06 GMT

PhyloD

References

Z. Brumme, C. Brumme, D. Heckerman, B. Korber, M. Daniels, J. Carlson, C. Kadie,T. Bhattacharya, C. Chui, T. Mo, R. Hogg, J. Montaner, N. Frahm, C. Brander, B. Walker, P. Harrigan. Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1. PLoS Pathogens, 3(7): e94, July 2007.

Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie,Jonathan Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber. Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations. Science 16 March 2007: Vol. 315. no. 5818, pp. 1583 - 1586

J. Carlson, C. Kadie,S. Mallal, and D. Heckerman. Leveraging hierarchical population structure in discrete association studies. PLoS ONE, 2(7): e591, July 2007.

Web Version, including some general information

http://atom.research.microsoft.com/bio/phylod.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: PhyloTree\PhyloTree.sln
Build directory: PhyloTree\PhyloD\bin\Release
Build directory: PhyloTree\Tabulate\bin\Release

Solution file: PhyloTree\PhyloDCCS.sln
Build directory: PhyloTree\PhyloDCcs\bin\Release

Solution file: PhyloTree\PhyloDDNsln
Build directory: PhyloTree\PhyloDDN\bin\Release

Exe's:

PhyloD.exe

Regression Test: PhyloTree\PhyloD\RegressionTest

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

PhyloDCcs.exe
PhyloDDN.exe

Regression Test: PhyloTree\PhyloDDN\RegressionTest

How to run regression tests

UPDATED WIKI: PhyloD

CarlK — Thu, 15 Nov 2007 16:45:03 GMT

PhyloD

Reference

Z. Brumme, C. Brumme, D. Heckerman, B. Korber, M. Daniels, J. Carlson, C. Kadie,T. Bhattacharya, C. Chui, T. Mo, R. Hogg, J. Montaner, N. Frahm, C. Brander, B. Walker, P. Harrigan. Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1. PLoS Pathogens, 3(7): e94, July 2007.

Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie,Jonathan Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber. Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations. Science 16 March 2007: Vol. 315. no. 5818, pp. 1583 - 1586

J. Carlson, C. Kadie,S. Mallal, and D. Heckerman. Leveraging hierarchical population structure in discrete association studies. PLoS ONE, 2(7): e591, July 2007.

Web Version, including some general information

http://atom.research.microsoft.com/bio/phylod.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: PhyloTree\PhyloTree.sln
Build directory: PhyloTree\PhyloD\bin\Release
Build directory: PhyloTree\Tabulate\bin\Release

Solution file: PhyloTree\PhyloDCCS.sln
Build directory: PhyloTree\PhyloDCcs\bin\Release

Solution file: PhyloTree\PhyloDDNsln
Build directory: PhyloTree\PhyloDDN\bin\Release

Exe's:

PhyloD.exe

Regression Test: PhyloTree\PhyloD\RegressionTest

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

PhyloDCcs.exe
PhyloDDN.exe

Regression Test: PhyloTree\PhyloDDN\RegressionTest

How to run regression tests

UPDATED WIKI: PhyloD

CarlK — Thu, 15 Nov 2007 16:44:27 GMT

PhyloD

Reference

Z. Brumme, C. Brumme, D. Heckerman, B. Korber, M. Daniels, J. Carlson, C. Kadie,T. Bhattacharya, C. Chui, T. Mo, R. Hogg, J. Montaner, N. Frahm, C. Brander, B. Walker, P. Harrigan. Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1. PLoS Pathogens, 3(7): e94, July 2007.

Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie,Jonathan Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber. Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations. Science 16 March 2007: Vol. 315. no. 5818, pp. 1583 - 1586

J. Carlson, C. Kadie,S. Mallal, and D. Heckerman. Leveraging hierarchical population structure in discrete association studies. PLoS ONE, 2(7): e591, July 2007.

Web Version, including some general information

http://atom.research.microsoft.com/bio/phylod.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: PhyloTree\PhyloTree.sln
Build directory: PhyloTree\PhyloD\bin\Release
Build directory: PhyloTree\Tabulate\bin\Release

Solution file: PhyloTree\PhyloDCCS.sln
Build directory: PhyloTree\PhyloDCcs\bin\Release

Solution file: PhyloTree\PhyloDDNsln
Build directory: PhyloTree\PhyloDDN\bin\Release

Exe's:

PhyloD.exe

Regression Test: PhyloTree\PhyloD\RegressionTest

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

PhyloDCcs.exe
PhyloDDN.exe

Regression Test: PhyloTree\PhyloDDN\RegressionTest

How to run regression tests

UPDATED WIKI: HLA Assignment

CarlK — Thu, 15 Nov 2007 16:40:44 GMT

HLA Assignment

References

J. Listgarten,N. Frahm, C. Kadie,C. Brander, D. Heckerman.A statistical framework for modeling HLA-dependent T cell response data, PLoS Computational Biology, 3(10): e188, October 2007.

N. Frahm, K. Yusim, T. Suscovich, S. Adams, J. Sidney, P. Hraber, H. Hewitt, Ca. Linde, D. Kavanagh, T. Woodberry, L. Henry, K. Faircloth, J. Listgarten,C. Kadie,N. Jojic,K. Sango, N. Brown, E. Pae, M. Zaman, F. Bihl, A. Khatri, M. John, S. Mallal, F. Marincola, B. Walker, A. Sette, D. Heckerman,B. Korber, C. Brander. Extensive HLA class I allele promiscuity among viral CTL epitopes.European Journal of Immunology, 37, August 2007.

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: HLA Assignment

CarlK — Thu, 15 Nov 2007 16:39:35 GMT

HLA Assignment

References

J. Listgarten, N. Frahm, C. Kadie, C. Brander, D. Heckerman. A statistical framework for modeling HLA-dependent T cell response data, PLoS Computational Biology, 3(10): e188, October 2007.

N. Frahm, K. Yusim, T. Suscovich, S. Adams, J. Sidney, P. Hraber, H. Hewitt, Ca. Linde, D. Kavanagh, T. Woodberry, L. Henry, K. Faircloth, J. Listgarten, C. Kadie, N. Jojic, K. Sango, N. Brown, E. Pae, M. Zaman, F. Bihl, A. Khatri, M. John, S. Mallal, F. Marincola, B. Walker, A. Sette, D. Heckerman, B. Korber, C. Brander. Extensive HLA class I allele promiscuity among viral CTL epitopes. European Journal of Immunology, 37, August 2007.

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: HLA Assignment

CarlK — Thu, 15 Nov 2007 16:38:00 GMT

HLA Assignment

References

J. Listgarten, N. Frahm, C. Kadie, C. Brander, D. Heckerman. A statistical framework for modeling HLA-dependent T cell response data, PLoS Computational Biology, 3(10): e188, October 2007.

N. Frahm, K. Yusim, T. Suscovich, S. Adams, J. Sidney, P. Hraber, H. Hewitt, Ca. Linde, D. Kavanagh, T. Woodberry, L. Henry, K. Faircloth, J. Listgarten, C. Kadie, N. Jojic, K. Sango, N. Brown, E. Pae, M. Zaman, F. Bihl, A. Khatri, M. John, S. Mallal, F. Marincola, B. Walker, A. Sette, D. Heckerman, B. Korber, C. Brander. Extensive HLA class I allele promiscuity among viral CTL epitopes. European Journal of Immunology, 37, August 2007.

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: HLA Assignment

CarlK — Thu, 15 Nov 2007 16:37:07 GMT

HLA Assignment

References

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: HLA Assignment

CarlK — Thu, 15 Nov 2007 16:35:11 GMT

HLA Assignment

References

J. Listgarten, N. Frahm, C. Kadie, C. Brander, D. Heckerman. A statistical framework for modeling HLA-dependent T cell response data, PLoS Computational Biology, 3(10): e188, October 2007.

N. Frahm, K. Yusim, T. Suscovich, S. Adams, J. Sidney, P. Hraber, H. Hewitt, Ca. Linde, D. Kavanagh, T. Woodberry, L. Henry, K. Faircloth, J. Listgarten, C. Kadie,, N. Jojic, K. Sango, N. Brown, E. Pae, M. Zaman, F. Bihl, A. Khatri, M. John, S. Mallal, F. Marincola, B. Walker, A. Sette, D. Heckerman, B. Korber, C. Brander. Extensive HLA class I allele promiscuity among viral CTL epitopes. European Journal of Immunology, 37, August 2007.

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: HLA Assignment

CarlK — Thu, 15 Nov 2007 01:16:38 GMT

HLA Assignment

References

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests

UPDATED WIKI: HLA Assignment

CarlK — Thu, 15 Nov 2007 01:16:23 GMT

HLA Assignment

References

J. Listgarten, N. Frahm, C. Kadie, , C. Brander, D. Heckerman. A statistical framework for modeling HLA-dependent T cell response data, PLoS Computational Biology, 3(10): e188, October 2007.

N. Frahm, K. Yusim, T. Suscovich, S. Adams, J. Sidney, P. Hraber, H. Hewitt, Ca. Linde, D. Kavanagh, T. Woodberry, L. Henry, K. Faircloth, J. Listgarten, C. Kadie, N. Jojic, K. Sango, N. Brown, E. Pae, M. Zaman, F. Bihl, A. Khatri, M. John, S. Mallal, F. Marincola, B. Walker, A. Sette, D. Heckerman, B. Korber, C. Brander. Extensive HLA class I allele promiscuity among viral CTL epitopes. EJI, 37, August 2007.

Web Version, including general information

http://atom.research.microsoft.com/bio/hlaassign.aspx

Pre-Compiled Programs for Windows

http://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx

Source Code Files

(To download see Source Code tab above)

Solution file: Qmr\HlaAssign.sln
Build directory: Qmr\HlaAssign\HlaAssignCCS\bin\Release

Exe's:

HlaAssign.exe

Regression test

Tabulate.exe

Regression Test: PhyloTree\Tabulate\RegressionTest

HlaAssignCcs.exe

How to run regression tests