SDIWG:NCBC Software Classification MAGNet Examples - Revision history

Aris at 04:52, 15 May 2007

2007-05-15T04:52:34Z

Aris: /* GRASP2 */

2007-05-13T22:25:54Z

GRASP2

Aris at 22:23, 13 May 2007

2007-05-13T22:23:35Z

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Aris at 22:26, 11 May 2007

2007-05-11T22:26:52Z

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2007-05-11T04:22:10Z

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Aris at 14:47, 10 May 2007

2007-05-10T14:47:44Z

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===DelPhi===
* Description: DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast (the best relaxation parameter is estimated at run time), accurate (calculation of the electrostatic free energy is less dependent on the resolution of the lattice) and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions.
* Input (parameters & Data Types): DelPhi takes as input a coordinate file format of a molecule or equivalent data for geometrical objects and/or charge distributions
* Output Data (parameters & Data Types): electrostatic potential in and around the system
* Implementation Language: Fortran and C
* Version, Date, Stage: Stable public release
* Authors: E.Alexov, R.Fine, M.K.Gilson, A.Nicholls, W.Rocchia, K.Sharp, and B. Honig.
* Platforms Tested: Unix-SGI IRIX, linux, PC (requires Fortran and C compilers), AIX IBM version and Mac.
* License: Freely available to academia; pay model for commercial users.
* Keywords: Finite Difference Poisson-Boltzman Solver
* URL: http://trantor.bioc.columbia.edu/delphi

@@ Line 71: / Line 71: @@
 * '''Organization''': MAGNet
 * '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Protein Modeling and Classification --> Molecular Visualization Package
 ===PrISM===
@@ Line 132: / Line 133: @@
 ===MEDUSA and Gorgon===
-* '''Description''': MEDUSA is an algorithm for learning predictive models of transcriptional gene regulation from gene expression and promoter sequence data.  By using a statistical learning approach based on boosing, MEDUSA learns cis regulatory motifs, condition-specific regulators, and regulatory programs that predict the differential expression of target genes.  The regulatory program is specified as an alternating decision tree (ADT).  The Java implementation of MEDUSA will allow a number of visualizations of the regulatory program and other inferred regulatory information, implemented in the accompanying Gorgon tool, including hits of significant and condition-specific motifs along the promoter sequences of target genes and regulatory network figures viewable in Cytoscape.
+* '''Description''': MEDUSA is an algorithm for learning predictive models of transcriptional gene regulation from gene expression and promoter sequence data.  By using a statistical learning approach based on boosting, MEDUSA learns cis regulatory motifs, condition-specific regulators, and regulatory programs that predict the differential expression of target genes.  The regulatory program is specified as an alternating decision tree (ADT).  The Java implementation of MEDUSA allows a number of visualizations of the regulatory program and other inferred regulatory information, implemented in the accompanying Gorgon tool, including hits of significant and condition-specific motifs along the promoter sequences of target genes and regulatory network figures viewable in Cytoscape.
 * '''Data Input''': Discretized (up/down/baseline) gene expression data in plain text format, promoter sequences in FASTA format, list of candidate transcriptional regulators and signal transducers in plain text format.
 * '''Data Output''': Regulatory program represented as a Java serialized object file readable by Gorgon and as a human readable XML file.  Gorgon currently generates views of learned PSSMs, positional hits along promoter sequences, and views of the ADT as HTML files, and generates network figures as Cytoscape format files.
@@ Line 143: / Line 144: @@
 * '''URL''': http://www.cs.columbia.edu/compbio/medusa (MATLAB),http://compbio.sytes.net:8090/medusa (Java beta version)
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Genomic & Phenotypic Analysis --> Regulatory/Signaling network reconstruction
 ===String kernel package===
@@ Line 157: / Line 158: @@
 * '''URL''': http://www.cs.columbia.edu/compbio/string-kernels
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Protein Modeling and Classification
 ===MatrixREDUCE===
@@ Line 171: / Line 172: @@
 * '''URL''': http://www.bussemakerlab.org/software/MatrixREDUCE
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Genomic & Phenotypic Analysis --> Regulatory/Signaling network reconstruction
@@ Line 186: / Line 187: @@
 * '''URL''': http://www.t-profiler.org
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Genomic & Phenotypic Analysis --> Network characterization
 ===TranscriptionDetector===
@@ Line 212: / Line 213: @@
 * '''License''':  n/a
 * '''Keywords''': Phenotypic integration, computational phenotypes
-* '''URL''': www.phenogo.org
+* '''URL''': http://www.phenogo.org
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Biotool --> Data Management --> Information retrieval, traversal and querying; Atomic --> SoftwareFunction --> Natural Language Processing
 ===MINDY===

@@ Line 70: / Line 70: @@
 * '''URL''': http://trantor.bioc.columbia.edu/grasp2
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''': SoftwareFunction --> Protein Modeling and Classification --> Molecular Visualization Package
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Protein Modeling and Classification --> Molecular Visualization Package
 ===PrISM===

@@ Line 272: / Line 272: @@
 * '''URL''': http://www.geworkbench.org
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Genomic & Phenotypic Analysis, Atomic --> SoftwareFunction --> Interaction Modeling, Atomic --> SoftwareFunction --> Protein Modeling and Classification, Atomic --> SoftwareFunction --> Software Engineering and Development Tool --> Integration --> Resource Integration Components, Atomic --> SoftwareFunction --> Software Engineering and Development Tool --> Integration --> Grid Computing Resources, Atomic --> SoftwareFunction --> Visualization
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Genomic & Phenotypic Analysis; Atomic --> SoftwareFunction --> Interaction Modeling; Atomic --> SoftwareFunction --> Protein Modeling and Classification; Atomic --> SoftwareFunction --> Software Engineering and Development Tool --> Integration --> Resource Integration Components; Atomic --> SoftwareFunction --> Software Engineering and Development Tool --> Integration --> Grid Computing Resources; Atomic --> SoftwareFunction --> Visualization

← Older revision		Revision as of 21:39, 13 May 2007
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	* '''Organization''': MAGNet		* '''Organization''': MAGNet
	* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Genomic & Phenotypic Analysis --> Regulatory/Signaling network reconstruction		* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Genomic & Phenotypic Analysis --> Regulatory/Signaling network reconstruction
		+
		+
		+	===geWorkbench===
		+	* '''Description''': geWorkbench is a Java application that provides users with an integrated suite of genomics tools. It is built on an open-source, extensible architecture that promotes interoperability and simplifies the development of new as well as the incorporation of pre-existing components. The resulting system provides seamless access to a multitude of both local and remote data and computational services through an integrated environment that offers a unified user experience. Over 50 data analysis and visualization components have been developed for the framework, covering a wide range of genomics domains including gene expression, sequence, structure and network data.
		+	* '''Data Input''': Gene epxression data (Affy, GenPix, RMA), Sequence (FASTA), Structure (PDB).
		+	* '''Data Output''': Analysis results (multiple formats).
		+	* '''Implementation Language''': Java
		+	* '''Version, Date, Stage''': 1.0.5, 3/23/07, stable production release
		+	* '''Authors''': A. Califano, A. Floratos. M. Kustagi, K. Smith, J. Watkinson, M. Hall, K. Keshav, X. Zhang, K. Kushal, B. Jagla, E. Daly, M. VanGinhoven, P. Morozov.
		+	* '''Platforms Tested''': Windows XP, Linux, Mac OS 10.x.
		+	* '''License''': Free.
		+	* '''Keywords''': Analysis suite, gene expression analysis, sequence analysis, network reconstruction, structure predcition, visualization.
		+	* '''URL''': http://www.geworkbench.org
		+	* '''Organization''': MAGNet
		+	* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Genomic & Phenotypic Analysis, Atomic --> SoftwareFunction --> Interaction Modeling, Atomic --> SoftwareFunction --> Protein Modeling and Classification, Atomic --> SoftwareFunction --> Software Engineering and Development Tool --> Integration --> Resource Integration Components, Atomic --> SoftwareFunction --> Software Engineering and Development Tool --> Integration --> Grid Computing Resources, Atomic --> SoftwareFunction --> Visualization

← Older revision		Revision as of 21:18, 13 May 2007
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	* '''Organization''': MAGNet		* '''Organization''': MAGNet
	* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Interaction Modeling		* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Interaction Modeling
		+
		+	===ARACNE===
		+	* '''Description''': ARACNE is an algorithm for inferring gene regulatory networks from a set of microarray experiments. The method uses mutual information to identify genes that are co-expressed and then applies the data processing inequality to filter out interactions that are likely to be indirect.
		+	* '''Data Input''': Text file containing measurements from a set of microarray experiments.
		+	* '''Data Output''': Text file containing predicted interactions.
		+	* '''Implementation Language''': C++, Java
		+	* '''Version, Date, Stage''': Version 1, June, 2006
		+	* '''Authors''': Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A.
		+	* '''Platforms Tested''': Window, Linux
		+	* '''License''': Open source
		+	* '''Keywords''': Reverse engineering, mutual information, genetic networks, microarray
		+	* '''URL''': http://amdec-bioinfo.cu-genome.org/html/ARACNE.htm
		+	* '''Organization''': MAGNet
		+	* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Genomic & Phenotypic Analysis --> Regulatory/Signaling network reconstruction

← Older revision		Revision as of 22:26, 11 May 2007
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	* '''Organization''': MAGNet		* '''Organization''': MAGNet
	* '''NCBC Ontology Classification''':		* '''NCBC Ontology Classification''':
		+
		+	===MINDY===
		+	* '''Description''': Given a transcription factor of interest, MINDY uses a large set of gene expression profile data to identify potential post-transcriptional modulators of the transcription factor's activity. MINDY is based on a three-way statistical interaction model that captures the post-transcriptional regulatory event where the ability of a transcription factor to activate/repress its target genes is monotonically controlled by a potential modulator gene.
		+	* '''Data Input''': Gene expression data in the EXP format, and a user-specified transcription factor of interest
		+	* '''Data Output''': Lists of the putative modulators and target genes of the transcription factor, and the modulatory interactions involving them
		+	* '''Implementation Language''': C++ and MATLAB, Java
		+	* '''Version, Date, Stage''': Stable release, April 2007
		+	* '''Authors''': Kai Wang, Ilya Nemenman, Adam Margolin, Riccardo Dalla-Favera, Andrea Califano
		+	* '''Platforms Tested''': Linux, Cygwin
		+	* '''License''': n/a
		+	* '''Keywords''': gene expression, transcriptional interaction, modulator
		+	* '''URL''': n/a
		+	* '''Organization''': MAGNet
		+	* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Genomic & Phenotypic Analysis --> Regulatory/Signaling network reconstruction
		+
		+	===B Cell Interactome===
		+	* '''Description''': The B cell interactome (BCI) is a network of protein-protein, protein-DNA and modulatory interactions in human B cells. The network contains known interactions (reported in public databases) and predicted interactions by a Bayesian evidence integration framework which integrates a variety of generic and context specific experimental clues about protein-protein and protein-DNA interactions - such as a large collection of B cell expression profiles - with inferences from different reverse engineering algorithms, such as GeneWays and ARACNE. Modulatory interactions are predicted by MINDY, an algorithm for the prediction of modulators of transcriptional interactions.
		+	* '''Data Input''': n/a
		+	* '''Data Output''': text file of binary interations associated with a probability.
		+	* '''Implementation Language''': Perl
		+	* '''Version, Date, Stage''': Version 2, March 2007
		+	* '''Authors''': Lefebvre C, Lim WK, Basso K, Dalla Favera R, and Califano A.
		+	* '''Platforms Tested''': n/a
		+	* '''License''':
		+	* '''Keywords''': Naive Bayes, Mixed-Interaction Network, human B cells.
		+	* '''URL''': http://amdec-bioinfo.cu-genome.org/html/BCellInteractome.html
		+	* '''Organization''': MAGNet
		+	* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Interaction Modeling

@@ Line 11: / Line 11: @@
 * '''URL''': http://trantor.bioc.columbia.edu/delphi
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Protein Modeling and Classification --> Numerical Calculation of Electrostatic Potential
 ===GRASP===
@@ Line 25: / Line 26: @@
 * '''URL''': http://trantor.bioc.columbia.edu/grasp
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Protein Modeling and Classification --> Molecular Visualization Package
 ===Nest===
@@ Line 39: / Line 40: @@
 * '''URL''': http://honiglab.cpmc.columbia.edu/cgi-bin/jackal/nest.cgi
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Protein Modeling and Classification --> Homology Modeling
 ===JACKAL===
@@ Line 53: / Line 55: @@
 * '''URL''': http://trantor.bioc.columbia.edu/programs/jackal
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Protein Modeling and Classification --> Prediction of Side-chain Conformations
 ===GRASP2===
@@ Line 67: / Line 70: @@
 * '''URL''': http://trantor.bioc.columbia.edu/grasp2
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': SoftwareFunction --> Protein Modeling and Classification --> Molecular Visualization Package
 ===PrISM===
@@ Line 81: / Line 85: @@
 * '''URL''': http://trantor.bioc.columbia.edu/programs/PrISM/
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Protein Modeling and Classification --> Homology Modeling
 ===Protein-DNA interface alignment===
@@ Line 95: / Line 100: @@
 * '''URL''': http://trantor.bioc.columbia.edu/programs/intfc_aln
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Protein Modeling and Classification --> Prediction of Side-chain Conformations
 ===SURFace===
@@ Line 109: / Line 114: @@
 * '''URL''': http://trantor.bioc.columbia.edu/surf/
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Protein Modeling and Classification --> Caculation of Solvent Accessible Area
 ===Target Explorer===
@@ Line 123: / Line 129: @@
 * '''URL''': http://trantor.bioc.columbia.edu/Target_Explorer/
 * '''Organization''': MAGNet
-* '''NCBC Ontology Classification''':
+* '''NCBC Ontology Classification''': Atomic --> SoftwareFunction --> Genomic & Phenotypic Analysis--> Sequence Annotation
 ===MEDUSA and Gorgon===