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A database and web service for structural bioinformatics studies of transcription factor (TF)-DNA interactions. Various datasets can be generated based on one or more search options specified by users.

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• SciCrunch
• 13 years ago - by Anonymous

Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

A comprehensive collection of human transcription factor binding sites models. DNA sequences of TF binding regions obtained by both pregenomic and high-throughput methods were collected from existing databases and other public data. The ChIPMunk software was used to construct positional weight matrices. Four motif discovery strategies were tested based on different motif shape priors including flat and periodic priors associated with DNA helix pitch. A quality rating was manually assigned to each model based on known binding preferences. An appropriate TFBS model was selected for each TF, with similar models selected for related TFs. In any case only one model per TF was selected unless there was additional evidence for two distinct binding models or different stable modes of dimerization. All TFBS models and initial binding segments data used for motif discovery were mapped to UniPROT IDs.

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• SciCrunch
• 13 years ago - by Anonymous

The IARC Working Group Reports contain common minimum technical standards and protocols for Biological Resource Centres dedicated to Cancer Research. * Cover Page * Table of Contents * Working group participants * Preamble * Definitions * Roles of biological resource centres in cancer research * Recommendations for BRCs * Selected protocols * Annexes

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• SciCrunch
• 15 years ago - by Anonymous

A database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse. Currently, the database contains >2000 samples from >500 ChIP-seq and ChIP-chip experiments, representing a total of >170 proteins and >10,000,000 protein-DNA interactions (March 2014). A web server provides an interface for database query. Protein-DNA binding intensities can be retrieved from individual samples for user-provided genomic regions. The retrieved intensities can be used to cluster samples and genomic regions to facilitate exploration of combinatorial patterns, cell type dependencies, and cross-sample variability of protein-DNA interactions.

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• SciCrunch
• 13 years ago - by Anonymous

A software library for analyzing DNase-seq data.

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• SciCrunch
• 13 years ago - by Anonymous

Data portal that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations (May 2013). Each dataset has gone through a consistent analysis and quality control pipeline; therefore, users could evaluate the overall quality of each dataset before examining binding sites near their genes of interest. CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets. It also allows users to leave comments to facilitate data evaluation and update.

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• SciCrunch
• 13 years ago - by Anonymous

A database for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs (snoRNAs, tRNAs, snRNAs, etc.) and protein-coding genes from ChIP-Seq data. ChIPBase currently includes millions of transcription factor binding sites (TFBSs) among 6 species. ChIPBase provides several web-based tools and browsers to explore TF-lncRNA, TF-miRNA, TF-mRNA, TF-ncRNA and TF-miRNA-mRNA regulatory networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Data analysis service for gene-list enrichment analysis against a manual database. It allows users to input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The database integrates interaction data from ChIP-chip, ChIP-seq, ChIP-PET and DamID studies and contains 189,933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31,932 target genes.

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• SciCrunch
• 13 years ago - by Anonymous

A freely editable semantic wiki for community-based curation of the terms used in Neuroscience. Entries are curated and eventually incorporated into the formal NIFSTD ontology. NeuroLex also includes a Resource branch for community members to freely add neuroscience relevant resources that do not become part of NIFSTD ontology but rather make up the NIF Registry. As part of the NIF, we provide a simple search interface to many different sources of neuroscience information and data. To make this search more effective, we are constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g., neuron is a cell. These categories provide the means to perform more effective searches and also to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that we use to describe our data, e.g., anatomical terms, techniques, organism names. Because wikis provide an easy interface for communities to contribute their knowledge, we started the NeuroLex.

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• SciCrunch
• 15 years ago - by Anonymous

Simultaneous search across multiple literature indices, including PubMed and Open Access literature, it is one of the core resources of NIF accessed through the NIF search interface. Literature results are displayed under the Literature tab. Features: * Facet by Year, Author, and / or Journal * Option to search open access literature only * Sort by relevance or year * Snippets from the full text of the paper are included in search results where search term was found * LinkOuts are now provided for some papers. These mean that someone associated a reagent, piece of data, note/blog, etc., with this specific publication. * Searching within sections of articles is now possible within the open access literature. For more info, see, http://neuinfo.org/about/release_notes_4.5.shtm#search. * Annotate papers. Any user can submit a public comment or annotation of an open access paper through the DOMEO tool. For more information, see http://neuinfo.org/about/release_notes_4.5.shtm#annotate

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• SciCrunch
• 15 years ago - by Anonymous

Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch have assigned RRIDs which are used to cite resources in scientific manuscripts. SciCrunch Registry, formerly NIF Registry, provides resources catalog. Allows to add new resources. Allows edit existing resources after registration. Curators are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping contents current.

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• SciCrunch
• 13 years ago - by Anonymous

A free, fully featured, powerful, configurable and easy to maintain bioinformatics workstation that provides more than 500 bioinformatics programs on an Ubuntu Linux 12.04 LTS base. Install it or run it live. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can run a Bio-Linux system on Amazon EC2 or other cloud computing architectures by using CloudBioLinux.

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• SciCrunch
• 13 years ago - by Anonymous

Database of all of the publicly available, complete prokaryotic genomes. In addition to having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes. CMR offers a wide variety of tools and resources, all of which are available off of our menu bar at the top of each page. Below is an explanation and link for each of these menu options. * Genome Tools: Find organism lists as well as summary information and analyses for selected genomes. * Searches: Search CMR for genes, genomes, sequence regions, and evidence. * Comparative Tools: Compare multiple genomes based on a variety of criteria, including sequence homology and gene attributes. SNP data is also found under this menu. * Lists: Select and download gene, evidence, and genomic element lists. * Downloads: Download gene sequences or attributes for CMR organisms, or go to our FTP site. * Carts: Select genome preferences from our Genome Cart or download your Gene Cart genes. The Omniome is the relational database underlying the CMR and it holds all of the annotation for each of the CMR genomes, including DNA sequences, proteins, RNA genes and many other types of features. Associated with each of these DNA features in the Omniome are the feature coordinates, nucleotide and protein sequences (where appropriate), and the DNA molecule and organism with which the feature is associated. Also available are evidence types associated with annotation such as HMMs, BLAST, InterPro, COG, and Prosite, as well as individual gene attributes. In addition, the database stores identifiers from other centers such as GenBank and SwissProt, as well as manually curated information on each genome or each DNA molecule including website links. Also stored in the Omniome are precomputed homology data, called All vs All searches, used throughout the CMR for comparative analysis.

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• SciCrunch
• 16 years ago - by Anonymous

An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet.

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• SciCrunch
• 13 years ago - by Anonymous

A software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (1) to predict whether the factor has activating or repressive function; (2) to infer the factor''''s target genes; and (3) to identify the motif of the factor and its collaborators which might modulate the factor''''s activating or repressive function. BETA requires ~2GB RAM and 1h for the whole procedure. BETA may run on the web server at Cistrome or may be downloaded.

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• SciCrunch
• 13 years ago - by Anonymous

The International Neuroinformatics Coordinating Facility (INCF) Training in Neuroinformatics section provides a broad listing of educational and training opportunities in fields related to neuroinformatics.

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• SciCrunch
• 15 years ago - by Anonymous

Software program for probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.

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• SciCrunch
• 14 years ago - by Anonymous

NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties. NEURON has benefited from judicious revision and selective enhancement, guided by feedback from the growing number of neuroscientists who have used it to incorporate empirically-based modeling into their research strategies. NEURON's computational engine employs special algorithms that achieve high efficiency by exploiting the structure of the equations that describe neuronal properties. It has functions that are tailored for conveniently controlling simulations, and presenting the results of real neurophysiological problems graphically in ways that are quickly and intuitively grasped. Instead of forcing users to reformulate their conceptual models to fit the requirements of a general purpose simulator, NEURON is designed to let them deal directly with familiar neuroscience concepts. Consequently, users can think in terms of the biophysical properties of membrane and cytoplasm, the branched architecture of neurons, and the effects of synaptic communication between cells. * helps users focus on important biological issues rather than purely computational concerns * has a convenient user interface * has a user-extendable library of biophysical mechanisms * has many enhancements for efficient network modeling * offers customizable initialization and simulation flow control * is widely used in neuroscience research by experimentalists and theoreticians * is well-documented and actively supported * is free, open source, and runs on (almost) everything

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• SciCrunch
• 13 years ago - by Anonymous

A tissue resource center which facilitates research into the relationship between Alzheimer's disease and other brain disorders such as strokes and mental illnesses. Most donations have been obtained from Alzheimer's patients. Normal controls are available, many of which are from subjects with close relatives with Alzheimer's. The Brown BTRC also supports a collection of brain tumor cases that were harvested from patients who underwent surgery and who were enrolled in a clinical trial for the development of new treatments for brain cancer.

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• SciCrunch
• 15 years ago - by Anonymous