Cytoscape Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. David States data management, microarray, information refining, natural language processing, molecular interactions, gene expression regulation, network visualization, open source Biotool - Data Management - Information retrieval, traversal and querying; Atomic - Software Function - Genomic & Phenotypic Analysis - Network characterization; Atomic - Software Function - Genomic & Phenotypic Analysis - Regulatory/Signaling network reconstruction; Atomic - Software Function - Natural Language Processing; Atomic - Biological Concept; Atomic - Software Function - Interaction Modeling; Atomic - Software Function - Visualization - Graph Viewers; Atomic - Software Type - Analytical NCIBI http://www.cytoscape.org/ MEAD MEAD is a publicly available toolkit for multi-lingual summarization and evaluation. The toolkit implements multiple summarization algorithms (at arbitrary compression rates) such as position-based, Centroid[RJB00], TF*IDF, and query-based methods. Methods for evaluating the quality of the summaries include co-selection (precision/recall, kappa, and relative utility) and content-based measures (cosine, word overlap, bigram overlap). Dragomir Radev document summarization, natural language processing Atomic - Software Function - Natural Language Processing Linux, MacOS, UNIX, Windows Public Domain NCIBI http://www.summarization.com/mead/ X!Tandem X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification. This software has a very simple, sophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. Ron Beavis mass spectroscopy, proteomics Atomic - Software Function - Genomic & Phenotypic Analysis - Sequence Annotation; Atomic - Software Function - Proteomic Analysis - Sequence Annotation MacOS, UNIX, Windows NCIBI http://www.thegpm.org/TANDEM/ MBI MBI is a backend repository of molecular sequences and sequence based annotation from a variety of public repositories. Zach Wright data management, interactive database Data - Measurement - Molecular interaction; Atomic - Software Type - Database NCIBI LexRank Demo We introduce a stochastic graph-based method for computing relative importance of textual units for Natural Language Processing. We test the technique on the problem of Text Summarization (TS). Extractive TS relies on the concept of sentence salience to identify the most important sentences in a document or set of documents. Salience is typically defined in terms of the presence of particular important words or in terms of similarity to a centroid pseudo-sentence. We consider a new approach, LexRank, for computing sentence importance based on the concept of eigenvector centrality in a graph representation of sentences. In this model, a connectivity matrix based on intra-sentence cosine similarity is used as the adjacency matrix of the graph representation of sentences. Our system, based on LexRank ranked in first place in more than one task in the recent DUC 2004 evaluation. In this paper we present a detailed analysis of ou! r approach and apply it to a larger data set including data from earlier DUC evaluations. We discuss several methods to compute centrality using the similarity graph. The results show that degree-based methods (including LexRank) outperform both centroid-based methods and other systems participating in DUC in most of the cases. Furthermore, the LexRank with threshold method outperforms the other degree-based techniques including continuous LexRank. We also show that our approach is quite insensitive to the noise in the data that may result from an imperfect topical clustering of documents. Dragomir Radev document summarization, natural language processing Atomic - Software Function - Natural Language Processing NCIBI http://tangra.si.umich.edu/~radev/lexrank/ SAGA SAGA stands for Subgraph Index for Approximate Graph Alignment. It is an efficient tool for approximate subgraph matching. SAGA allows users to match a query graph against a large database of graphs. At the core of SAGA is a flexible graph distance model that incorporates node approximate matching as well as approximate structure matching. A powerful indexing method is implemented to speed up the matching process. Some applications of SAGA include querying/comparing pathways and querying parsed biomedical literature databases to find similar documents. Jignesh Patel Atomic - Algorithm; Atomic - Software Function - Graph Analysis NCIBI http://enigma.eecs.umich.edu/saga.html GenePattern GenePattern is a powerful analysis workflow tool developed to support multidisciplinary genomic research programs and designed to encourage rapid integration of new techniques. 3.0 2007-05-01 Linux, MacOS, Windows NCIBI http://www.broad.mit.edu/cancer/software/genepattern/index.html BCDE Biological Concept Diagram Editor (BCDE) is a tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes. Besides standard diagramming functions, it has powerful data capture and annotation capabilities. BCDE is compatible with BioPAX and it also exports to Powerpoint and Visio. Alpha molecular interactions, bioinformatics tools, workflows, Diagram Editor Biotool - Data Management - Knowledge Mining and Capturing Linux, MacOS, SunOS, UNIX, Windows NCIBI http://arrayanalysis.mbni.med.umich.edu/draw/ Cytoscape Plugin for MiMI This plugin retrieves and displays molecular interactions from Michigan Molecular Interactions (MiMI) database. Using this plugin, users can extend and edit current networks interactively, link out interactions to external web resources, edit interaction annotations and use cerebral layout. By integrating with NCIBI BioNlp and SAGA, users can get literature information associated with interactions and conduct graphic match against biological pathways. Jing Gao 1.0 2007-03-01 protein interaction, network visualization, XQuery, interactive database, information refining, molecular interactions, bioinformatics tools, Biotool - Data Management - Information retrieval, traversal and querying - Protein-Protein Interaction; Atomic - Software Function - Visualization - Interaction Network Java, Cytoscape, MSSQL Server, PHP NCIBI http://www.bioinformatics.med.umich.edu/app/nlp/logo/pluginHelp/pluginHelp.html Protege Open-source ontology editor and knowledge-based framework developed at Stanford (must subscribe) 3.1.1 bioinformatics tools, ontology Atomic - Software Function - Software Engineering and Development Tool - Ontology Development and Management HPUX, Java, Linux, MacOS, SunOS, UNIX, Windows NCIBI http://protege.stanford.edu/ SLIF SLIF finds fluorescence microscope images in on-line journal articles, and indexes them according to cell line, proteins visualized, and resolution. Dr. Robert F. Murphy NCIBI http://murphylab.web.cmu.edu/services/SLIF/ MiMI MiMI is an XML based molecular interactions database and front end. MiMI supports XQuery, Keyword, Forms based and CLI access. Glenn Tarcea 2.6 Release protein interaction, XQuery, molecular interactions, Pathway, keyword search Biotool/Data Management/Information retrieval, traversal and querying Windows Free for Non-commercial Use NCIBI http://mimi.ncibi.org/ MiSearch An interface to the NCBI Entrez systems that ranks query output based on the likelihood that you will click on an entry. Ranking is performed by building up a profile based on past user behavior. Multiple profiles per user can be defined. David States interactive database, information refining, natural language processing, keyword search, bioinformatics tools, journal articles, open source Biotool - Data Management - Information retrieval, traversal and querying; Dissemination Vehicle - Interactive Web-Based Tool; Atomic - Software Function - Natural Language Processing; Atomic - Software Type - Analytical NCIBI http://misearch.ncibi.org/ SNP Function Portal A web database with the goal of integrating SNP function annotation all public sources as well as those derived from various sequence/structure analysis programs. A powerful SNP search function, utilizing genomic and HapMap II data, provides the capability of finding any structurally and genetically SNPs. Fan Meng 0.2 data management, interactive database, document summarization, genomic sequence analysis, bioinformatics tools, snp, function, genome-wide scanning, hapmap Atomic - Software Function - Genomic & Phenotypic Analysis - Sequence Annotation NCIBI http://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/snpfunc.aspx Shannon NLP Tools Tools for automated named entity recognition and tagging, information retrieval and text summarization. David States data management, interactive database, information refining, document summarization, natural language processing, keyword search, bioinformatics tools Biotool - Data Management - Information retrieval, traversal and querying; Atomic - Algorithm; Atomic - Software Function - Genomic & Phenotypic Analysis - Network characterization; Atomic - Software Function - Natural Language Processing; Atomic - Software Type - Analytical NCIBI PMCOA Database SQL database with all open access articles from PubMed Central, sentence-segmented, citation network extracted, and named entity tagged for genes, proteins, and UMLS concepts. Updated monthly. Alex Ade interactive database, document summarization, natural language processing, journal articles Biotool - Data Management - Data Storage; Atomic - Document - Publication - Paper; Atomic - Software Function - Natural Language Processing; Atomic - Software Type - Database NCIBI ClairLib clair library for natural language processing, information retrieval, and network analysis Dragomir Radev Atomic - Software Function - Natural Language Processing NCIBI http://tangra.si.umich.edu/clair/clairlib/ PSLID PSLID provides a structured, well-annotated database of fluorescence microscope images depicting subcellular location proteins. Two interfaces are currently provided: a text and image content search interface, and a graphical interface for exploring location patterns grouped into Subcellular Location Trees. Dr. Robert F. Murphy NCIBI http://murphylab.web.cmu.edu/services/PSLID/ miniTUBA miniTUBA is a dynamic Bayesian network analysis tool designed for analyzing and interpreting molecular clinical data. Peter Woolf 0.9 information refining, gene expression regulation, bioinformatics tools Atomic - Software Function - Genomic & Phenotypic Analysis - Regulatory/Signaling network reconstruction; Atomic - Software Function - Statistical Analysis - Statistical Package; Atomic - Software Type - Analytical; Atomic - SoftwareFunction - Visualization - Interaction Network NCIBI http://www.minituba.org/ MarkerInfoFinder MarkerInfoFinder is a web-based Medline abstract search engine that supports the use of genetic marker IDs and flexible positional/linkage disequilibrium criteria. natural language processing, bioinformatics tools, snp Atomic - Software Function - Document Retrieval Linux, MacOS, Windows NCIBI http://brainarray.mbni.med.umich.edu/brainarray/ MarkIt Addresses the question "Which genes are differentially expressed across two treatments?" Dr. Peter Woolf 1.31 2006-10-24 Atomic - Software Function - Numerical Methods - Optimizers; Atomic - Software Function - Statistical Analysis - Statistical Package; Atomic - Software Type - Analytical NCIBI http://www-personal.umich.edu/~welchr/biomarker/ geWorkbench geWorkbench is an open-source bioinformatics platform that offers a comprehensive and extensible collection of tools for the management, analysis, visualization and annotation of biomedical data. Many kinds of analysis are supported - for microarrays, there are filtering and normalization, basic statistical analyses, clustering, network reverse engineering, as well as many common visualization tools. For sequence data there are routines such as BLAST, pattern detection, transcription factor mapping, and syntenic region analysis. Furthermore, genomic sequences around markers of interest found in microarray experiments can be easily retrieved and, for example, used for promoter/transcription factor analysis. 1.0.3 2005-05-15 bioinformatics tools, workflows Data - Measurement - Molecular Interaction; Biotool - Data Management - Information retrieval, traversal and querying; Atomic - Software Function - Genomic & Phenotypic Analysis - Regulatory/Signaling network reconstruction; Atomic - Software Function - Genomic & Phenotypic Analysis - Sequence Similarity Searching; Atomic - Software Function - Interaction Modeling - Protein interaction modeling; Atomic - Software Function - Software Engineering and Development Tool - Integration - Grid Computing Resources; Atomic - Software Function - Software Engineering and Development Tool - Integration - Resource Integration Components; Atomic - Software Function - Statistical Analysis; Atomic - Software Function - Visualization; Atomic - Software Type - Analytical; Atomic - Software Type - Database; Atomic - Software Type - Toolkit Linux, MacOS, Windows NCIBI http://wiki.c2b2.columbia.edu/workbench/index.php/Main_Page miBLAST A common task in many modern bioinformatics applications is to match a set of nucleotide query sequences against a large sequence dataset. Exis-ting tools, such as BLAST, are designed to evaluate a single query at a time and can be unacceptably slow when the number of sequences in the query set is large. In this paper, we present a new algorithm, called miBLAST, that evaluates such batch workloads efficiently. At the core, miBLAST employs a q-gram filtering and an index join for efficiently detecting similarity between the query sequences and database sequences. This set-oriented technique, which indexes both the query and the database sets, results in substantial performance improvements over existing methods. Our results show that miBLAST is significantly faster than BLAST in many cases. For example,! miBLAST aligned 247 965 oligonucleotide sequences in the Affymetrix probe set against the Human UniGene in 1.26 days, compared with 27.27 days with BLAST (an improvement by a factor of 22). The relative performance of miBLAST increases for larger word sizes; however, it decreases for longer queries. miBLAST employs the familiar BLAST statistical model and output format, guaranteeing the same accuracy as BLAST and facilitating a seamless transition for existing BLAST users. Jignesh Patel 1.0 2005-08-01 microarray, BLAST Atomic - Software Function - Genomic & Phenotypic Analysis - Sequence Similarity Searching; Atomic - Algorithm Linux Educational Community License (free for all uses) NCIBI http://www.eecs.umich.edu/miblast/ Marimba Marimba is a web based static Bayesian network analysis tool designed for analyzing and interpreting gene expression data. Peter Woolf microarray, information refining, bioinformatics tools Atomic - Software Function - Genomic & Phenotypic Analysis - Regulatory/Signaling network reconstruction; Atomic - Software Function - Statistical Analysis - Statistical Package; Atomic - Software Type - Analytical NCIBI http://helab.bioinformatics.med.umich.edu/marimba/ Oncomine A resource for examining gene expression in cancer. The goal of the project is to collect, standardize, analyze, and deliver published cancer gene expression data to the research community. Probe the expression of a gene across thousands of cancer samples or explore genes, processes, and pathways deregulated in a particular type of cancer. Oncomine pre-computes cancer profiles, clusters, and gene set modules so you can focus on discovery. 3.0 microarray, cancer, gene expression regulation, function, genome-wide scanning Biotool - Data Management - Information retrieval, traversal and querying NCIBI http://www.oncomine.org/main/index.jsp tfblast A tool written by David States to identify transcription factor recognition sites in large collections of genomic sequence. Also implements a statistical clustering analysis to identify regions of high binding site density. Also includes a CpG island search. David States gene expression regulation, transcription factor, genomic sequence analysis, bioinformatics tools Atomic - Biological Concept - Genome; Atomic - Biological Concept - Gene; Atomic - Biological Concept - DNA; Atomic - Data Typology - Biological Sequence; Atomic - Software Function - Genomic & Phenotypic Analysis - Regulatory/Signaling network reconstruction; Atomic - Software Type - Analytical NCIBI Bubble Bubble is a Bayesian network working environment that integrates public data, user data, and solicits relevant user feedback. Currently this is an early beta form. Peter Woolf microarray, bioinformatics tools Atomic - Software Function - Genomic & Phenotypic Analysis - Regulatory/Signaling network reconstruction; Atomic - Software Function - Numerical Methods - Optimizers; Atomic - Software Function - Statistical Analysis - Statistical Package; Atomic - Software Type - Analytical; Atomic - Visualization - Interactive network analysis NCIBI http://bubble.engin.umich.edu BioSearch-2D A web based visual corpus summarization system for biomedical literature. Carlos Santos data management, interactive database, information refining, document summarization, natural language processing, keyword search, bioinformatics tools Biotool - Data Management - Information retrieval, traversal and querying; Dissemination Vehicle - Interactive Web-Based Tool; Atomic - Software Function - Genomic & Phenotypic Analysis - Network characterization; Atomic - Software Function - Natural Language Processing; Atomic - Software Type - Analytical Microsoft SQL Server, PHP, Apache, Javascript NCIBI WGAS The Web-based GeneChip Analysis System (WGAS) incorporates popular probe-, gene- and function category-level analysis methods through straightforward web interface. It natively supports custom GeneChip probe set definition files for more accurate data interpretation. Users can also access to any Cel files deposited in NCBI GEO database for re-analysis and comparison. Manhong Dai data management, microarray, gene expression regulation, snp, collaboration, file sharing Biotool - Data Management - Information retrieval, traversal and querying NCIBI http://arrayanalysis.mbni.med.umich.edu/arrayanalysis.html GIN - Gene Interaction Network GIN - Gene Interaction Network Dragomir Radev Atomic - Software Function - Natural Language Processing NCIBI http://belobog.si.umich.edu:8080/gin/ PubMed Database SQL database with all PubMed baseline and update records, sentence-segmented and named entity tagged for genes, proteins, and MeSH terms. Contains over 17 million citations from Medline and other life sciences journals. Updated nightly. Alex Ade 07n interactive database, document summarization, natural language processing, journal articles NCIBI Custom CDF Genome-wide expression profiling is a powerful tool for implicating novel gene ensembles in cellular mechanisms of health and disease. The most popular platform for genome-wide expression profiling is the Affymetrix GeneChip. However, its selection of probes relied on earlier genome and transcriptome annotation which is significantly different from current knowledge. The resultant informatics problems have a profound impact on analysis and interpretation the data. Here, we address these critical issues and offer a solution. We identified several classes of problems at the individual probe level in the existing annotation, under the assumption that current genome and transcriptome databases are more accurate than those used for GeneChip design. We then reorganized probes on more than a dozen popular GeneChips into gene-, transcript- and exon-specific probe sets in light of up-to-date genome, cDNA/EST clustering and single nucleotide polymorphism information. Comparing analysis results between the original and the redefined probe sets reveals ~30?50% discrepancy in the genes previously identified as differentially expressed, regardless of analysis method. Our results demonstrate that the original Affymetrix probe set definitions are inaccurate, and many conclusions derived from past GeneChip analyses may be significantly flawed. It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions. Manhong Dai 7.0 2006-05-01 Atomic - Software Function - Genomic & Phenotypic Analysis - Sequence Annotation NCIBI http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp PDG-ACE Java program that identifies relationships between pairs of genes in input gene blocks (based on genetic linkage peaks). These relationships are based on common elements or features of the gene descriptions. Richard Mc Eachin disease genes, genetic linkage, common feature NCIBI