Bioinformatics - Revision history

Deadline: added GATK

2015-02-19T14:13:50Z

added GATK

← Older revision		Revision as of 10:13, 19 February 2015
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	* [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.		* [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.
	* [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).		* [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).
			* [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.

Deadline: moved autodock to bioinformatics page

2009-07-21T20:32:15Z

moved autodock to bioinformatics page

← Older revision		Revision as of 16:32, 21 July 2009
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	* [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.		* [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.
	* [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).		* [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).
	*[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.

Deadline at 20:08, 17 July 2009

2009-07-17T20:08:35Z

← Older revision		Revision as of 16:08, 17 July 2009
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	* [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.		* [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.
	* [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).		* [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).
	*[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.		*[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.
	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.

Deadline: added mpihmmer

2009-07-17T20:07:45Z

added mpihmmer

← Older revision		Revision as of 16:07, 17 July 2009
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	*[http://mpiblast.~~lanl~~.gov/ mpiBLAST]		* [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.
	*[http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock]		* [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).
			*[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.

Bli at 21:22, 14 February 2006

2006-02-14T21:22:53Z

New page

*[http://mpiblast.lanl.gov/ mpiBLAST]
*[http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock]