Source Code Biol Med Volume 3; 2008

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Volume 3; 2008

Brief Reports

Analysis by siRNA_profile program displays novel thermodynamic characteristics of highly functional siRNA molecules

Pirkko Muhonen, Ranga N Parthasarathy, Anthony J Janckila, Kalman G Büki, and H Kalervo Väänänen

Source Code Biol Med. 2008; 3: 8. Published online 2008 May 21. doi: 10.1186/1751-0473-3-8.

PMCID: PMC2424050

| Abstract | Full Text | PDF–426K |

FASH: A web application for nucleotides sequence search

Isana Veksler-Lublinksy, Danny Barash, Chai Avisar, Einav Troim, Paul Chew, and Klara Kedem

Source Code Biol Med. 2008; 3: 9. Published online 2008 May 27. doi: 10.1186/1751-0473-3-9.

PMCID: PMC2426692

| Abstract | Full Text | PDF–597K |

Methodology

Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data

Nicolas J Parker and Andrew G Parker

Source Code Biol Med. 2008; 3: 5. Published online 2008 April 18. doi: 10.1186/1751-0473-3-5.

PMCID: PMC2374781

CRANKITE: A fast polypeptide backbone conformation sampler

Alexei A Podtelezhnikov and David L Wild

Source Code Biol Med. 2008; 3: 12. Published online 2008 June 24. doi: 10.1186/1751-0473-3-12.

PMCID: PMC2443148

| Abstract | Full Text | PDF–741K |

Boolean network simulations for life scientists

István Albert, Juilee Thakar, Song Li, Ranran Zhang, and Réka Albert

Source Code Biol Med. 2008; 3: 16. Published online 2008 November 14. doi: 10.1186/1751-0473-3-16.

PMCID: PMC2603008

| Abstract | Full Text | PDF–557K |

Research

Epigrass: a tool to study disease spread in complex networks

Flávio C Coelho, Oswaldo G Cruz, and Cláudia T Codeço

Source Code Biol Med. 2008; 3: 3. Published online 2008 February 26. doi: 10.1186/1751-0473-3-3.

PMCID: PMC2275240

The MERG Suite: Tools for discovering competencies and associated learning resources

Ravi Teja Bhupatiraju, William R Hersh, Valerie Smothers, Michael Fordis, and Peter S Greene

Source Code Biol Med. 2008; 3: 7. Published online 2008 May 14. doi: 10.1186/1751-0473-3-7.

PMCID: PMC2416363

| Abstract | Full Text | PDF–712K |

Wndchrm – an open source utility for biological image analysis

Lior Shamir, Nikita Orlov, D Mark Eckley, Tomasz Macura, Josiah Johnston, and Ilya G Goldberg

Source Code Biol Med. 2008; 3: 13. Published online 2008 July 8. doi: 10.1186/1751-0473-3-13.

PMCID: PMC2478650

| Abstract | Full Text | PDF–261K |

Software Reviews

Faunus: An object oriented framework for molecular simulation

Mikael Lund, Martin Trulsson, and Björn Persson

Source Code Biol Med. 2008; 3: 1. Published online 2008 February 1. doi: 10.1186/1751-0473-3-1.

PMCID: PMC2266748

| Abstract | Full Text | PDF–684K |

LSID Tester, a tool for testing Life Science Identifier resolution services

Roderic DM Page

Source Code Biol Med. 2008; 3: 2. Published online 2008 February 18. doi: 10.1186/1751-0473-3-2.

PMCID: PMC2276318

| Abstract | Full Text | PDF–524K |

A Perl toolkit for LIMS development

James A Morris, Simon A Gayther, Ian J Jacobs, and Christopher Jones

Source Code Biol Med. 2008; 3: 4. Published online 2008 March 19. doi: 10.1186/1751-0473-3-4.

PMCID: PMC2322998

| Abstract | Full Text | PDF–201K |

The Multiscale Systems Immunology project: software for cell-based immunological simulation

Faheem Mitha, Timothy A Lucas, Feng Feng, Thomas B Kepler, and Cliburn Chan

Source Code Biol Med. 2008; 3: 6. Published online 2008 April 28. doi: 10.1186/1751-0473-3-6.

PMCID: PMC2426691

Flow: Statistics, visualization and informatics for flow cytometry

Jacob Frelinger, Thomas B Kepler, and Cliburn Chan

Source Code Biol Med. 2008; 3: 10. Published online 2008 June 17. doi: 10.1186/1751-0473-3-10.

PMCID: PMC2442075

| Abstract | Full Text | PDF–1.5M |

OSPACS: Ultrasound image management system

Will Stott, Andy Ryan, Ian J Jacobs, Usha Menon, Conrad Bessant, and Christopher Jones

Source Code Biol Med. 2008; 3: 11. Published online 2008 June 20. doi: 10.1186/1751-0473-3-11.

PMCID: PMC2442597

| Abstract | Full Text | PDF–285K |

Microbial Diagnostic Array Workstation (MDAW): a web server for diagnostic array data storage, sharing and analysis

Joy Scaria, Aswathy Sreedharan, and Yung-Fu Chang

Source Code Biol Med. 2008; 3: 14. Published online 2008 September 23. doi: 10.1186/1751-0473-3-14.

PMCID: PMC2563012

| Abstract | Full Text | PDF–511K |

Permutation – based statistical tests for multiple hypotheses

Anyela Camargo, Francisco Azuaje, Haiying Wang, and Huiru Zheng

Source Code Biol Med. 2008; 3: 15. Published online 2008 October 21. doi: 10.1186/1751-0473-3-15.

PMCID: PMC2611984

Other Issues: previous | next | latest | archive

		Other Issues: previous \| next \| latest \| archive Volume 3; 2008 Brief Reports Analysis by siRNA_profile program displays novel thermodynamic characteristics of highly functional siRNA molecules Pirkko Muhonen, Ranga N Parthasarathy, Anthony J Janckila, Kalman G Büki, and H Kalervo Väänänen Source Code Biol Med. 2008; 3: 8. Published online 2008 May 21. doi: 10.1186/1751-0473-3-8. PMCID: PMC2424050 \| Abstract \| Full Text \| PDF–426K \| FASH: A web application for nucleotides sequence search Isana Veksler-Lublinksy, Danny Barash, Chai Avisar, Einav Troim, Paul Chew, and Klara Kedem Source Code Biol Med. 2008; 3: 9. Published online 2008 May 27. doi: 10.1186/1751-0473-3-9. PMCID: PMC2426692 \| Abstract \| Full Text \| PDF–597K \| Methodology Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data Nicolas J Parker and Andrew G Parker Source Code Biol Med. 2008; 3: 5. Published online 2008 April 18. doi: 10.1186/1751-0473-3-5. PMCID: PMC2374781 \| Abstract \| Full Text \| PDF–359K \| Supplementary Material \| CRANKITE: A fast polypeptide backbone conformation sampler Alexei A Podtelezhnikov and David L Wild Source Code Biol Med. 2008; 3: 12. Published online 2008 June 24. doi: 10.1186/1751-0473-3-12. PMCID: PMC2443148 \| Abstract \| Full Text \| PDF–741K \| Boolean network simulations for life scientists István Albert, Juilee Thakar, Song Li, Ranran Zhang, and Réka Albert Source Code Biol Med. 2008; 3: 16. Published online 2008 November 14. doi: 10.1186/1751-0473-3-16. PMCID: PMC2603008 \| Abstract \| Full Text \| PDF–557K \| Research Epigrass: a tool to study disease spread in complex networks Flávio C Coelho, Oswaldo G Cruz, and Cláudia T Codeço Source Code Biol Med. 2008; 3: 3. Published online 2008 February 26. doi: 10.1186/1751-0473-3-3. PMCID: PMC2275240 \| Abstract \| Full Text \| PDF–2.3M \| Supplementary Material \| The MERG Suite: Tools for discovering competencies and associated learning resources Ravi Teja Bhupatiraju, William R Hersh, Valerie Smothers, Michael Fordis, and Peter S Greene Source Code Biol Med. 2008; 3: 7. Published online 2008 May 14. doi: 10.1186/1751-0473-3-7. PMCID: PMC2416363 \| Abstract \| Full Text \| PDF–712K \| Wndchrm – an open source utility for biological image analysis Lior Shamir, Nikita Orlov, D Mark Eckley, Tomasz Macura, Josiah Johnston, and Ilya G Goldberg Source Code Biol Med. 2008; 3: 13. Published online 2008 July 8. doi: 10.1186/1751-0473-3-13. PMCID: PMC2478650 \| Abstract \| Full Text \| PDF–261K \| Software Reviews Faunus: An object oriented framework for molecular simulation Mikael Lund, Martin Trulsson, and Björn Persson Source Code Biol Med. 2008; 3: 1. Published online 2008 February 1. doi: 10.1186/1751-0473-3-1. PMCID: PMC2266748 \| Abstract \| Full Text \| PDF–684K \| LSID Tester, a tool for testing Life Science Identifier resolution services Roderic DM Page Source Code Biol Med. 2008; 3: 2. Published online 2008 February 18. doi: 10.1186/1751-0473-3-2. PMCID: PMC2276318 \| Abstract \| Full Text \| PDF–524K \| A Perl toolkit for LIMS development James A Morris, Simon A Gayther, Ian J Jacobs, and Christopher Jones Source Code Biol Med. 2008; 3: 4. Published online 2008 March 19. doi: 10.1186/1751-0473-3-4. PMCID: PMC2322998 \| Abstract \| Full Text \| PDF–201K \| The Multiscale Systems Immunology project: software for cell-based immunological simulation Faheem Mitha, Timothy A Lucas, Feng Feng, Thomas B Kepler, and Cliburn Chan Source Code Biol Med. 2008; 3: 6. Published online 2008 April 28. doi: 10.1186/1751-0473-3-6. PMCID: PMC2426691 \| Abstract \| Full Text \| PDF–1.2M \| Supplementary Material \| Flow: Statistics, visualization and informatics for flow cytometry Jacob Frelinger, Thomas B Kepler, and Cliburn Chan Source Code Biol Med. 2008; 3: 10. Published online 2008 June 17. doi: 10.1186/1751-0473-3-10. PMCID: PMC2442075 \| Abstract \| Full Text \| PDF–1.5M \| OSPACS: Ultrasound image management system Will Stott, Andy Ryan, Ian J Jacobs, Usha Menon, Conrad Bessant, and Christopher Jones Source Code Biol Med. 2008; 3: 11. Published online 2008 June 20. doi: 10.1186/1751-0473-3-11. PMCID: PMC2442597 \| Abstract \| Full Text \| PDF–285K \| Microbial Diagnostic Array Workstation (MDAW): a web server for diagnostic array data storage, sharing and analysis Joy Scaria, Aswathy Sreedharan, and Yung-Fu Chang Source Code Biol Med. 2008; 3: 14. Published online 2008 September 23. doi: 10.1186/1751-0473-3-14. PMCID: PMC2563012 \| Abstract \| Full Text \| PDF–511K \| Permutation – based statistical tests for multiple hypotheses Anyela Camargo, Francisco Azuaje, Haiying Wang, and Huiru Zheng Source Code Biol Med. 2008; 3: 15. Published online 2008 October 21. doi: 10.1186/1751-0473-3-15. PMCID: PMC2611984 \| Abstract \| Full Text \| PDF–323K \| Supplementary Material \|
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