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http://claire.bardel.free.fr/software.html
Software package to perform phylogeny based association and localization analysis.Used for association detection and localization of susceptibility sites using haplotype phylogenetic trees. Performs these two phylogeny-based analysis: tests association between candidate gene and disease; pinpoints markers (SNPs) that are putative disease susceptibility loci.
Proper citation: ALTree (RRID:SCR_007562) Copy
http://organelledb.lsi.umich.edu/
Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light.
Proper citation: Organelle DB (RRID:SCR_007837) Copy
It provides information on natural and artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families. The PMD is based on literature, and each entry in the database corresponds to one article which may describe one, several or a number of protein mutants. Each database entry is identified by a serial number and is defined as either natural or artificial, depending on the type of the mutation. For each entry the following are recorded : JOURNAL, TITLE, CROSS-REFERENCE, PROTEIN, N-TERMINAL, CHANGE, FUNCTION, STRUCTURE, STABILITY, etc. CROSS-REFERENCE indicates the code names of the protein given in other databases such as Protein Identification Resources (2). N-TERMINAL shows the N-terminal sequence of five amino acids which may help to show the unambiguous numbering of th e sequence. CHANGE indicates the position and kind of mutations, such as amino acid substitution, insertion and deletion, denoted with a specific notation. Any functional or structural features (FUNCTION, STRUCTURE, STABILITY,etc) observed in the mutant are described immediately after ''CHANGE''. Relative differences in activity and/or stability, in comparison with the wild-type protein, are indicated with symbols (- -),(-),(=),(+) or (+ +). Complete loss of activity is denoted as (0). Data Submission A data submission system was newly prepared in the PMD. We welcome the authors of articles published in academic journals to submit their own mutant data to the PMD. After checking the contents, we will register the data with a unique accession number.
Proper citation: Protein Mutant Database (RRID:SCR_007878) Copy
STRFPak is a Matlab toolbox for estimating the linear and nonlinear stimulus-response mapping function of sensory systems. This mapping function is commonly called the spatio- or spectro-temporal receptive field (STRF). A quantitative estimate of the STRF can be used in subsequent computational modeling studies or to predict future responses of the system. STRFPak implements several general STRF estimation techniques and can be used with any stimuli (including natural scenes and sounds). The theoretical basis for STRF estimation has been known for some time, but estimation software has not been widely available. This project aims to develop appropriate software and make it available to the wider community of sensory neuroscientists. Although STRFPak is based on established methods it incorporates two important innovations. First, STRFPak can be used to characterize a sensory system from its response to arbitrary stimuli including natural signals (e.g., vocalizations, natural scenes). Second, STRFPak incorporates several methods for estimating nonlinear STRFs. STRFPak also includes tutorial examples and documentation.
Proper citation: Spatio- Spectro- Temporal Receptive Field (RRID:SCR_007995) Copy
http://www.nactem.ac.uk/genia/
Resources and tools from a project to automatically extract useful information from texts written by scientists to help overcome the problems caused by information overload. The primary annotated resource created is the GENIA corpus, a collection of biomedical literature which consists of multiple layers of annotation, encompassing both syntactic and semantic annotation. The project also created or coordinated the annotation of multiple other corpus resources. Additionally, a rich set of automatic tools are available for various annotation tasks, most trained on various parts of the GENIA corpus annotations. The GENIA corpus was developed to provide a reference material for the development of bio-TM systems. The corpus currently contains 1,999 Medline abstracts which were collected using the three MeSH terms, human, blood cells, and transcription factors. The corpus has been annotated with various levels of linguistic and semantic information. The GENIA corpus includes the following: * POS annotation * Treebank * Coreference Annotation * Term annotation * Event annotation * Relation annotation * Cellular localization * Disease-Gene association * Pathway corpus The GENIA Project initiated the BioNLP Shared Task series and has organized a number of tasks in three different shared task events, many using resources based on GENIA Corpus annotations. Tools include: * XConc suite: a collection of XML-based tools which are integrated to support the corpus development and annotation.
Proper citation: GENIA Project: Mining literature for knowledge in molecular biology (RRID:SCR_007990) Copy
A computational hosting resource which assissts with lab organization by splitting functions into four modules. “Order requests” is a module where users can view and track order requests. The module “Inventory” allows users to track commercial and lab-made products. “Documents” allows users to organize and share protocols and other documents. “Equipment sign-up” allows users to manage shared equipment. An active help system, video guides, and 1-on-1 demos are available for assistance when setting up.
Proper citation: Quartzy (RRID:SCR_007992) Copy
http://compgen.bio.unipd.it/bioinfo/
Welcome to the computational genomics laboratory''s home page. Main research interests: computational biology, bioinformatics and systems biology applied to the study of the mechanisms underlying gene expression regulation. They also develop bioinformatic software aiming at helping the research community solve some problems.
Proper citation: Computational Genomics Laboratory (RRID:SCR_007901) Copy
Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. The EBI Gene Expression Atlas Blog discusses ideas, features and problems of creating a large scale meta-analytical atlas of gene expression from publicly available microarray data. Atlas REST API provides all the results available in the main web application in a pragmatic, easy to use form - simple HTTP GET queries as input and either JSON or XML formats as output. Gene Expression Atlas goals: 1. Provision of a statistically robust framework for integration of gene expression experiment results across different platforms at a meta-analytical level 2. A simple interface for identifying strong differential expression candidate genes in conditions of interest 3. Integration of ontologies for high quality annotation of gene and sample attributes 4. Construction of new gene expression summarized views, with a view to analysis of putative signaling pathway targets, discovery of correlated gene expression patterns and the identification of condition/tissue-specific patterns of gene expression.
Proper citation: Gene Expression Atlas (RRID:SCR_007989) Copy
http://people.biochem.umass.edu/sfournier/fournierlab/snornadb/
A database of S. cerevisiae H/ACA and C/D box snoRNAs, useful for research on rRNA nucleotide modifications in the ribosome, especially those created by small nucleolar RNA:protein complexes (snoRNPs). The interactive service enables a user to visualize the positions of pseudouridines, 2'-O-methylations, and base methylations in three-dimensional space in the ribosome and also in linear and secondary structure formats of ribosomal RNA. The tools provide additional perspective on where the modifications occur relative to functional regions within the rRNA and relative to other nearby modifications. This package of tools is presented as a major enhancement of an existing but significantly upgraded yeast snoRNA database. The other key features of the enhanced database include details of the base pairing of snoRNAs with target RNAs, genomic organization of the yeast snoRNA genes, and information on corresponding snoRNAs and modifications in other model organisms.
Proper citation: Yeast snoRNA Database (RRID:SCR_007980) Copy
Public university in the Brazilian state of São Paulo. It is the largest Brazilian public university.
Proper citation: University of Sao Paulo; Sao Paulo; Brazil (RRID:SCR_007979) Copy
http://www.ensembl.org/info/docs/tools/vep/index.html
Data analysis service to predict the functional consequences of known and unknown variants.
Proper citation: Variant Effect Predictor (RRID:SCR_007931) Copy
A database which supports high-throughput NMR and MS approaches to the identification and quantification of metabolites present in biological samples. MMCD serves as a hub for information on small molecules of biological interest gathered from electronic databases and the scientific literature. Each metabolite entry in the MMCD is supported by information in separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available, NMR chemical shifts determined by empirical and/or theoretical approaches, calculated isotopomer masses, information on the presence of the metabolite in different biological species, and links to images, references, and other public databases. The MMCD search engine supports versatile data mining and allows users to make individual or bulk queries on the basis of experimental NMR and/or MS data plus other criteria.
Proper citation: Madison Metabolomics Consortium Database (RRID:SCR_007803) Copy
http://purl.bioontology.org/ontology/DERMO
Ontology of human dermatologic disease
Proper citation: Human Dermatological Disease Ontology (RRID:SCR_007648) Copy
Database of gene expression in whole-mount mouse embryos derived from in situ hybridization on mid-gestation mouse embryos. A genome wide screening for genes showing a tissue restricted expression pattern in mid-gestation embryos is performed to identify genes that are likely to play an important role in the regulatory networks controlling pattern formation and organogenesis. The screening provides the basis for imaging the molecular anatomy of the mouse embryo, and for creating a gene resource for a directed functional analysis of developmental processes. The experimental protocol is available. Pattern genes in MAMEP: 1912 Images in MAMEP: 23994
Proper citation: MAMEP - Molecular Anatomy of the Mouse Embryo Project (RRID:SCR_007768) Copy
Database of information about restriction enzymes and related proteins containing published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Several tools are available including REBsites, BLAST against REBASE, NEBcutter and REBpredictor. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. Users may submit new enzyme and/or sequence information, recommend references, or send them corrections to existing data. The contents of REBASE may be browsed from the web and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email.,
Proper citation: REBASE (RRID:SCR_007886) Copy
A research center associated with the University of Pittsburgh that specializes in the diagnosis of Alzheimer's disease and related disorders. The overall objective of the ADRC is to study the pathophysiology of Alzheimer's disease, with the aim of improving the reliability of diagnosis of Alzheimer's and developing effective treatment strategies. Current research foci emphasize neuropsychiatry and neuropsychology, molecular genetics and epidemiology, basic neuroscience, and structural and functional imaging that aid in the diagnosis and treatment of Alzheimer's disease. Specific services at the ADRC include: comprehensive diagnostic evaluation of patients with suspected Alzheimer's disease and other forms of dementia; evaluation of memory, language, judgment, and other cognitive abilities; and education and counseling for patients and families.
Proper citation: University of Pittsburgh Alzheimer Disease Research Center (RRID:SCR_008084) Copy
http://www.cs.cmu.edu/~dst/HHsim/
A graphical simulation of a section of excitable neuronal membrane using the Hodgkin-Huxley equations. It provides full access to the Hodgkin-Huxley parameters, membrane parameters, stimulus parameters, and ion concentrations. In contrast with NEURON or GENESIS, which are vastly more sophisticated research tools, HHsim is simple educational software designed specifically for graduate or undergraduate neurophysiology courses. The user interface can be mastered in a couple of minutes and provides many ways for the student to experiment. Also included are sample exercises that use the simulator. HHsim is available as a Windows, Mac, or Unix executable file that does not require a Matlab license. Source code is included. It is also available in source-only form if you have Matlab R2007a or later. The latest release of HHsim is version 3.1, released February 16, 2008.
Proper citation: HHsim: Graphical Hodgkin-Huxley Simulator (RRID:SCR_008087) Copy
Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. Consists of RNA sequencing and exon microarray data profiling up to sixteen cortical and subcortical structures across full course of human brain development, high resolution neuroanatomical transcriptional profiles of about 300 distinct structures spanning entire brain for four midgestional prenatal specimens, in situ hybridization image data covering selected genes and brain regions in developing and adult human brain, reference atlas in full color with high resolution anatomic reference atlases of prenatal (two stages) and adult human brain along with supporting histology, magnetic resonance imaging (MRI) and diffusion weighted imaging (DWI) data.
Proper citation: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) (RRID:SCR_008083) Copy
A low-level specification for describing mathematics as a basis for machine to machine communication, developed by the W3C.
Proper citation: MathML (RRID:SCR_008078) Copy
Repository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource.
Proper citation: CellML Model Repository (RRID:SCR_008113) Copy
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