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http://hazmap.nlm.nih.gov/

Occupational health database designed for health and safety professionals and for consumers seeking information about the adverse effects of workplace exposures to chemical and biological agents. The main links in Haz-Map are between chemicals and occupational diseases. These links have been established using current scientific evidence. Haz-Map shows the diseases linked to each agent and the agents linked to each disease. Agents are chemical such as formaldehyde, or biological such as grain dust. Haz-Map links jobs and hazardous job tasks with occupational diseases and their symptoms. In Haz-Map, chronic occupational diseases are linked to both jobs and industries, while acute diseases and infectious diseases are linked only to jobs. Cancers are not linked to jobs, industries or findings. The information in Haz-Map comes from textbooks, journal articles, the Documentation of the Threshold Limit Values (published by ACGIH), and electronic databases such as NLM's Hazardous Substances Data Bank (HSDB). Haz-Map staff classifies, summarizes, and regularly updates the information found in the database.

Proper citation: Haz-Map: Occupational Exposure to Hazardous Agents (RRID:SCR_002365) Copy   

•   Source: SciCrunch Registry
  

http://www.pubgene.org/

It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate.

Proper citation: PubGene (RRID:SCR_002119) Copy   

•   Source: SciCrunch Registry
  

http://cpdb.molgen.mpg.de

An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered.

Proper citation: ConsensusPathDB (RRID:SCR_002231) Copy   

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http://www.genscript.com/psort/wolf_psort.html

Data analysis service for protein subcellular localization prediction.

Proper citation: WoLF PSORT (RRID:SCR_002472) Copy   

•   Source: SciCrunch Registry
  

https://pfam.xfam.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. iPfam is a resource that describes physical interactions between those Pfam domains that have a representative structure in the Protein DataBank (PDB). When two or more domains occur within a single structure, the domains are analysed to see if they form an interaction. If the domains are close enough to form an interaction, the bonds that play a role in that interaction are determined. The goal has been to re-calculate iPfam interaction data for each new Pfam release, so that, as Pfam changes, the information within iPfam remains up to date.

Proper citation: Protein families database of alignments and HMMs (RRID:SCR_002115) Copy   

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http://compbio.cs.toronto.edu/psmdb

Database of non-redundant sets of protein - small-molecule complexes that are especially suitable for structure-based drug design and protein - small-molecule interaction research. PSMB supports: * Support frequent updates - The number of new structures in the PDB is growing rapidly. In order to utilize these structures, frequent updates are required. In contrast to manual procedures which require significant time and effort per update, generation of the PSMDB database is fully automatic thereby facilitating frequent database updates. * Consider both protein and ligand structural redundancy - In the database, two complexes are considered redundant if they share a similar protein and ligand (the protein - small-molecule non-redundant set). This allows the database to contain structural information for the same protein bound to several different ligands (and vice-versa). Additionally, for completeness, the database contains a set of non-redundant complexes when only protein structural redundancy is considered (our protein non-redundant set). The following images demonstrate the structural redundancy of the protein complexes in the PDB compared to the PSMDB. * Efficient handling of covalent bonds -Many protein complexes contain covalently bound ligands. Typically, protein-ligand databases discard these complexes; however, the PSMDB simply removes the covalently bound ligand from the complex, retaining any non-covalently bound ligands. This increases the number of usable complexes in the database. * Separate complexes into protein and ligand files -The PSMDB contains individual structure files for both the protein and all non-covalently bound ligands. The unbound proteins are in PDB format while the individual ligands are in SDF format (in their native coordinate frame).

Proper citation: Protein-Small Molecule Database (RRID:SCR_002112) Copy   

•   Source: SciCrunch Registry
  

http://www.dbass.soton.ac.uk/

A database of new exon boundaries induced by pathogenic mutations in human disease genes.

Proper citation: DBASS (RRID:SCR_002107) Copy   

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http://fullmal.hgc.jp/index_ajax.html

FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes. Sponsors: This database has been constructed and maintained by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science (JSPS). This work was also supported by a Special Coordination Funds for Promoting Science and Technology from the Science and Technology Agency of Japan (STA) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan.

Proper citation: Full-Malaria: Malaria Full-Length cDNA Database (RRID:SCR_002348) Copy   

•   Source: SciCrunch Registry
  

http://interactome.org/index.php/Main_Page

This Wiki page provides information about Interactome of various species. An interactome of a species provides an important clues on how to interpret metabolic pathways of constituent enzymes and global protein network, which facilitates in turn to understand the mechanism responsible for the cellular functions.

Proper citation: Interactome Wiki (RRID:SCR_000750) Copy   

•   Source: SciCrunch Registry
  

https://simulabeta.sourceforge.io/

Software tool as simulation program for insulin glucose feedback control. Based on nonlinear MiMe-NoCoDI model.

Proper citation: SimulaBeta (RRID:SCR_021900) Copy   

•   Source: SciCrunch Registry
  

https://github.com/QZH2022/germline_flow

High performance of GPU accelerated variant calling tool in genome data analysis.

Proper citation: germline flow (RRID:SCR_021906) Copy   

•   Source: SciCrunch Registry
  

https://github.com/vlink/marge

Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.

Proper citation: Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) Copy   

•   Source: SciCrunch Registry
  

http://bioinfo.jialab-ucr.org/CancerMIRNome/

Web server for cancer miRNome interactive analysis and visualization based on human miRNome data of cancer types from The Cancer Genome Atlas, and public cancer circulating miRNome profiling datasets from NCBI Gene Expression Omnibus and ArrayExpress. Comprehensive database for interactive analysis and visualization of miRNA expression profiles.

Proper citation: CancerMIRNome (RRID:SCR_022092) Copy   

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http://ceumass.eps.uspceu.es/

Software tool for searching metabolites in different databases including Kegg, HMDB, LipidMaps, Metlin, NP Atlas, KNApSAcK, MINE and in house library. Designed for searches through experimental masses obtained from mass spectrometry techniques. Metabolite annotation tool that uses expert system to score putative annotation based on analytical information acquired under different configurations.

Proper citation: CEU Mass Mediator (RRID:SCR_022090) Copy   

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https://www.microbialtec.com/aerobic-cultivation.html

Aerobic cultivation services to culture various microorganisms that can be isolated from readily available sources.

Proper citation: Creative Biogene Aerobic Cultivation Service Resource (RRID:SCR_022099) Copy   

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https://www.microbialtec.com/strain-anaerobic-culture.html

Service for anaerobic bacteria cultivation and culture using variety of culture media and culture conditions. Includes collection, strain cultivation, isolation, identification and strain preservation.

Proper citation: Creative Biogene Strain Anaerobic Culture Service Resource (RRID:SCR_022097) Copy   

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http://www.bioconductor.org/packages/release/bioc/html/qvalue.html

R package that takes a list of p-values resulting from the simultaneous testing of hypotheses and estimates their q-values. It is designed to measure the proportion of false positives when a test is significant. The software is capable of generating plots for visualization. It can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

Proper citation: Qvalue (RRID:SCR_001073) Copy   

•   Source: SciCrunch Registry
  

https://plueckthun.bioc.uzh.ch/antibody

AAAAA aims to become the ultimate tool for antibody structural analysis, modelling and engineering.

Proper citation: AHo’s Amazing Atlas of Antibody Anatomy (RRID:SCR_022095) Copy   

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http://toppcluster.cchmc.org/

A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.

Proper citation: ToppCluster (RRID:SCR_001503) Copy   

•   Source: SciCrunch Registry
  

https://sourceforge.net/projects/viste/

Open source, platform-independent application for the visualization and analysis of complex, high-dimensional imaging data such as Diffusion Tensor Imaging (DTI) and High Angular Resolution Diffusion Imaging (HARDI). It has a plugin-based architecture which allows third parties to develop new plugins to extend the tool. Overview of the many features: * vIST/e is programmed in C++. It uses the Visualization Toolkit for visualization and pipelined data processing, as well as the cross-platform toolkit Qt Framework for an easy-to-use Graphical User Interface. * vIST/e introduces a powerful new plugin system, which allows for modular development with increased extensibility and stability. * Powerful GPU-based visualization techniques allow for smooth, real-time visualization of large data sets. Using custom ray tracing algorithms created with OpenGL, vIST/e can render DTI ellipsoids and HARDI spherical harmonics glyphs up to 4th order. The high frame rates offered by modern GPU technology allows for interactive exploration of this complex data. * Diffusion Tensor Imaging data can be visualized and interactively explored in a number of ways, including multiple cross-sections, volume rendering, and tensor glyphs. Derived scalar volumes, including various different anisotropy measures, can be computed and visualized. Data from other modalities, such as structural MRI, can be shown alongside the DTI data. * Various fiber tracking methods allow for fast and accurate reconstruction of fiber pathways. Interactively defined Regions of Interest (ROIs) can be used for seeding and filtering of fibers. Fibers are visualized either as lines, optionally using a powerful, GPU-based lighting engine, or as 3D structures such as tubes. * Scalar volumes, glyphs, and fibers can be colored using a wide array of coloring option. Customizable color loop-up tables allow for highly flexible visualization of scalar data. * Visualization and processing of various different HARDI formats is supported. HARDI data is interactively visualized using highly detailed glyphs rendered on the GPU. HARDI glyphs can be visualized in combination with DTI glyphs, for a better overview of complex diffusion data. * vIST/e includes support for NVIDIA's Compute Unified Device Architecture (CUDA), which enables highly parallel, GPU-based data processing, allowing for significant speed-up of computationally expensive algorithms.

Proper citation: vIST/e (RRID:SCR_001627) Copy   

•   Source: SciCrunch Registry