https://www.clustermonkey.net/cdp/index.php?title=Bioinformatics&feed=atom&action=historyBioinformatics - Revision history2024-03-28T12:32:44ZRevision history for this page on the wikiMediaWiki 1.27.4https://www.clustermonkey.net/cdp/index.php?title=Bioinformatics&diff=2811&oldid=prevDeadline: added GATK2015-02-19T14:13:50Z<p>added GATK</p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* [http://www.mpiblast.org/ mpiBLAST] is a freely available, open-source, parallel implementation of [http://www.ncbi.nih.gov/blast/ NCBI BLAST]. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems. Lastly, a renewed focus and consolidation of the many codebases has positioned mpiBLAST to continue to be of high utility to the bioinformatics community.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* [http://www.mpiblast.org/ mpiBLAST] is a freely available, open-source, parallel implementation of [http://www.ncbi.nih.gov/blast/ NCBI BLAST]. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems. Lastly, a renewed focus and consolidation of the many codebases has positioned mpiBLAST to continue to be of high utility to the bioinformatics community.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* [http://mpihmmer.org/ MPI-HMMER] is an open source MPI implementation of the HMMER protein sequence analysis suite. The main search algorithms, hmmpfam and hmmsearch, have been ported to MPI in order to provide high throughput HMMER searches on modern computational clusters. MPI-HMMER has sophisticated I/O, a self-contained coordinator/worker model, and the easy inclusion of accelerated architectures (e.g. GP-GPUs).</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* [http://mpihmmer.org/ MPI-HMMER] is an open source MPI implementation of the HMMER protein sequence analysis suite. The main search algorithms, hmmpfam and hmmsearch, have been ported to MPI in order to provide high throughput HMMER searches on modern computational clusters. MPI-HMMER has sophisticated I/O, a self-contained coordinator/worker model, and the easy inclusion of accelerated architectures (e.g. GP-GPUs).</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [https://www.broadinstitute.org/gatk/ GATK] (The Genome Analysis Toolkit) is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.</ins></div></td></tr>
</table>Deadlinehttps://www.clustermonkey.net/cdp/index.php?title=Bioinformatics&diff=2226&oldid=prevDeadline: moved autodock to bioinformatics page2009-07-21T20:32:15Z<p>moved autodock to bioinformatics page</p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 20:32, 21 July 2009</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* [http://www.mpiblast.org/ mpiBLAST] is a freely available, open-source, parallel implementation of [http://www.ncbi.nih.gov/blast/ NCBI BLAST]. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems. Lastly, a renewed focus and consolidation of the many codebases has positioned mpiBLAST to continue to be of high utility to the bioinformatics community.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* [http://www.mpiblast.org/ mpiBLAST] is a freely available, open-source, parallel implementation of [http://www.ncbi.nih.gov/blast/ NCBI BLAST]. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems. Lastly, a renewed focus and consolidation of the many codebases has positioned mpiBLAST to continue to be of high utility to the bioinformatics community.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* [http://mpihmmer.org/ MPI-HMMER] is an open source MPI implementation of the HMMER protein sequence analysis suite. The main search algorithms, hmmpfam and hmmsearch, have been ported to MPI in order to provide high throughput HMMER searches on modern computational clusters. MPI-HMMER has sophisticated I/O, a self-contained coordinator/worker model, and the easy inclusion of accelerated architectures (e.g. GP-GPUs)<del class="diffchange diffchange-inline">. </del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [http://mpihmmer.org/ MPI-HMMER] is an open source MPI implementation of the HMMER protein sequence analysis suite. The main search algorithms, hmmpfam and hmmsearch, have been ported to MPI in order to provide high throughput HMMER searches on modern computational clusters. MPI-HMMER has sophisticated I/O, a self-contained coordinator/worker model, and the easy inclusion of accelerated architectures (e.g. GP-GPUs).</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">*[http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock] is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock actually consists of two main programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid re-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders</del>.</div></td><td colspan="2"> </td></tr>
</table>Deadlinehttps://www.clustermonkey.net/cdp/index.php?title=Bioinformatics&diff=2204&oldid=prevDeadline at 20:08, 17 July 20092009-07-17T20:08:35Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* [http://www.mpiblast.org/ mpiBLAST] is a freely available, open-source, parallel implementation of [http://www.ncbi.nih.gov/blast/ NCBI BLAST]. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems. Lastly, a renewed focus and consolidation of the many codebases has positioned mpiBLAST to continue to be of high utility to the bioinformatics community.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* [http://www.mpiblast.org/ mpiBLAST] is a freely available, open-source, parallel implementation of [http://www.ncbi.nih.gov/blast/ NCBI BLAST]. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems. Lastly, a renewed focus and consolidation of the many codebases has positioned mpiBLAST to continue to be of high utility to the bioinformatics community.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* [http://mpihmmer.org/ MPI-HMMER] is an open source MPI implementation of the HMMER protein sequence analysis suite. The main search algorithms, hmmpfam and hmmsearch, have been ported to MPI in order to provide high throughput HMMER searches on modern computational clusters. MPI-HMMER has sophisticated I/O, a self-contained coordinator/worker model, and the easy inclusion of accelerated architectures (e.g. GP-GPUs).  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* [http://mpihmmer.org/ MPI-HMMER] is an open source MPI implementation of the HMMER protein sequence analysis suite. The main search algorithms, hmmpfam and hmmsearch, have been ported to MPI in order to provide high throughput HMMER searches on modern computational clusters. MPI-HMMER has sophisticated I/O, a self-contained coordinator/worker model, and the easy inclusion of accelerated architectures (e.g. GP-GPUs).  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*[http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock] is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock actually consists of two main programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid re-calculates these grids.  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*[http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock] is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock actually consists of two main programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid re-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.</div></td><td colspan="2"> </td></tr>
</table>Deadlinehttps://www.clustermonkey.net/cdp/index.php?title=Bioinformatics&diff=2203&oldid=prevDeadline: added mpihmmer2009-07-17T20:07:45Z<p>added mpihmmer</p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 20:07, 17 July 2009</td>
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<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*[http://mpiblast.<del class="diffchange diffchange-inline">lanl</del>.gov/ mpiBLAST]</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [http://<ins class="diffchange diffchange-inline">www.</ins>mpiblast.<ins class="diffchange diffchange-inline">org/ mpiBLAST] is a freely available, open-source, parallel implementation of [http://www.ncbi.nih</ins>.gov/<ins class="diffchange diffchange-inline">blast/ NCBI BLAST]. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems. Lastly, a renewed focus and consolidation of the many codebases has positioned </ins>mpiBLAST <ins class="diffchange diffchange-inline">to continue to be of high utility to the bioinformatics community.</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*[http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock]</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">* [http://mpihmmer.org/ MPI-HMMER</ins>] <ins class="diffchange diffchange-inline">is an open source MPI implementation of the HMMER protein sequence analysis suite. The main search algorithms, hmmpfam and hmmsearch, have been ported to MPI in order to provide high throughput HMMER searches on modern computational clusters. MPI-HMMER has sophisticated I/O, a self-contained coordinator/worker model, and the easy inclusion of accelerated architectures (e.g. GP-GPUs). </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*[http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock] <ins class="diffchange diffchange-inline">is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock actually consists of two main programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid re-calculates these grids. </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.</ins></div></td></tr>
</table>Deadlinehttps://www.clustermonkey.net/cdp/index.php?title=Bioinformatics&diff=1621&oldid=prevBli at 21:22, 14 February 20062006-02-14T21:22:53Z<p></p>
<p><b>New page</b></p><div>*[http://mpiblast.lanl.gov/ mpiBLAST]<br />
*[http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock]</div>Bli