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http://www.phi-base.org/

Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).

Proper citation: PHI-base (RRID:SCR_003331) Copy   

•   Source: SciCrunch Registry

http://www.t-profiler.org

One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool

Proper citation: T-profiler (RRID:SCR_003452) Copy   

•   Source: SciCrunch Registry

http://dire.dcode.org

Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.

Proper citation: Distant Regulatory Elements (RRID:SCR_003058) Copy   

•   Source: SciCrunch Registry

http://epilepsy.uni-freiburg.de/database

A comprehensive database for human surface and intracranial EEG data that is suitable for a broad range of applications e.g. of time series analyses of brain activity. Currently, the EU database contains annotated EEG datasets from more than 200 patients with epilepsy, 50 of them with intracranial recordings with up to 122 channels. Each dataset provides EEG data for a continuous recording time of at least 96 hours (4 days) at a sample rate of up to 2500 Hz. Clinical patient information and MR imaging data supplement the EEG data. The total duration of EEG recordings included execeeds 30000 hours. The database is composed of different modalities: Binary files with EEG recording / MR imaging data and Relational database for supplementary meta data.

Proper citation: EPILEPSIE database (RRID:SCR_003179) Copy   

•   Source: SciCrunch Registry

http://www.mitomap.org/

Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf.

Proper citation: MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) Copy   

•   Source: SciCrunch Registry

http://mistdb.com

Database which contains the signal transduction proteins for complete and draft bacterial and archaeal genomes. The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes.

Proper citation: MiST - Microbial Signal Transduction database (RRID:SCR_003166) Copy   

•   Source: SciCrunch Registry

http://www.netpath.org/

A manually curated resource of signal transduction pathways in humans. All pathways are freely available for download in BioPAX level 3.0, PSI-MI version 2.5 and SBML version 2.1 formats. The slim pathway models representing only core reactions in each pathway are available at NetSlim. All the NetPath pathway models are also submitted to WikiPathways., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NetPath (RRID:SCR_003567) Copy   

•   Source: SciCrunch Registry

http://gwyddion.net/

Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry.

Proper citation: Gwyddion (RRID:SCR_015583) Copy   

•   Source: SciCrunch Registry

https://web.njit.edu/~matveev/calc.html

A modeling tool for simulating intracellular calcium diffusion and buffering. CalC solves continuous reaction-diffusion PDEs describing the entry of calcium into a volume through point-like channels, and its diffusion, buffering and binding to calcium receptors. Its features include: being platform-independent; being operated by simple script; combinable with MATLAB; and providing real-time views. Demos and manuals are provided on the website.

Proper citation: CalC (RRID:SCR_014259) Copy   

•   Source: SciCrunch Registry

https://www.mcgill.ca/bic/resources/omega

Open data repository fully dedicated to MEG data in raw and processed form. The archive also contains anatomical MRI volumes and demographic and questionnaire information. Organized and stored as the Brain Imaging Data Structure (BIDS) with the integration of multimodal electrophysiology data. Directly readable by data-analysis software with Brainstorm. OMEGA will continue to expand, with contributions from the scientific community.

Proper citation: Open MEG Archive (RRID:SCR_014930) Copy   

•   Source: SciCrunch Registry

http://www.novocraft.com/products/novoalign/

Software tool designed for mapping short reads onto a reference genome generated from Illumina, Ion Torrent, and 454 NGS platforms. Its features include paired end alignment, methylation status analysis, automatic base quality calibration, and in built adapter trimming and base quality trimming.

Proper citation: NovoAlign (RRID:SCR_014818) Copy   

•   Source: SciCrunch Registry

https://evidencemodeler.github.io/

Software tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format).

Proper citation: EVidenceModeler (RRID:SCR_014659) Copy   

•   Source: SciCrunch Registry

http://pasapipeline.github.io/

Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute.

Proper citation: PASA (RRID:SCR_014656) Copy   

•   Source: SciCrunch Registry

http://www.mbl.org/videoscribbler/vscrib.html

VideoScribbler is a program that makes it possible to trace directly onto live video. It was developed to provide a way to outline and count cells in a video image. The program displays the live video image in a 640x480 window. Userrs can click and drag the mouse to outline cells, while releasing the mouse button will complete the outline and increment the "Object Count" display at the bottom of the window.

Proper citation: Videoscribbler (RRID:SCR_013607) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://iidp.coh.org/Default.aspx

The goal of the Integrated Islet Distribution Program (IIDP) is to work with the leading islet isolation centers in the U.S. to distribute high quality human islets to the diabetes research community, in order to advance scientific discoveries and translational medicine.

Proper citation: Integrated Islet Distribution Program (IIDP) (RRID:SCR_014387) Copy   

•   Source: SciCrunch Registry

http://www.roslin.ed.ac.uk/alan-archibald/porcine-genome-sequencing-project/

Map of identifyied genes controlling traits of economic and welfare significance in the pig. The project objectives were to produce a genetic map with markers spaced at approximately 20 centiMorgan intervals over at least 90% of the pig genome; to produce a physical map with at least one distal and one proximal landmark locus mapped on each porcine chromosome arm and also genetically mapped; to develop a flow karyotype for the pig based on FACS sorted chromosomes; to develop PCR based techniques to enable rapid genotyping for polymorphic markers; to evaluate synteny conservation between pigs, man, mice and cattle; to develop and evaluate the statistical techniques required to analyze data from QTL mapping experiments and to plan and initiate the mapping of QTLs in the pig; to map loci affecting traits of economic and biological significance in the pig; and to develop the molecular tools to allow the future identification and cloning of mapped loci. Animal breeders currently assume that economically important traits such as growth, carcass composition and reproductive performance are controlled by an infinite number of genes each of infinitessimal effect. Although this model is known to be unrealistic, it has successfully underpinned the genetic improvement of livestock, including pigs, over recent decades. A map of the pig genome would allow the development of more realistic models of the genetic control of economic traits and the ultimately the identification of the major trait genes. This would allow the development of more efficient marker assisted selection which may be of particular value for traits such as disease resistance and meat quality.

Proper citation: Pig Genome Mapping (RRID:SCR_012884) Copy   

•   Source: SciCrunch Registry

http://www.mathworks.com/help/fuzzy/index.html

A software toolbox which provides MATLAB functions, apps, and a Simulink block for analyzing, designing, and simulating fuzzy logic systems. Fuzzy Logic Toolbox allows users to model complex system behaviors using simple logic rules, and then implement these rules in a user-designed fuzzy inference system. Functions are provided for many common methods, including fuzzy clustering and adaptive neurofuzzy learning. The toolbox can be used as a stand-alone fuzzy inference engine or in connection with Simulink. Different versions of the software are available for specific fuzzy inference systems.

Proper citation: Fuzzy Logic Toolbox (RRID:SCR_014268) Copy   

•   Source: SciCrunch Registry

https://github.com/nbcrrolls/workflows/tree/master/Production/AmberGPUMDSimulation

A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like.

Proper citation: Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) Copy   

•   Source: SciCrunch Registry

https://code.google.com/archive/p/edlut/

Simulation software which creates spiking cell models using either a time-driven strategy or an event-driven strategy based on look-up tables. EDLUT serves as a tool for studying the computational principles of neural systems to reveal how different functionalities of the brain and central nervous system are based on cell and topology properties.

Proper citation: EDLUT (RRID:SCR_014261) Copy   

•   Source: SciCrunch Registry

https://genomecenter.ucdavis.edu/core-facilities/

Genome Center uses technologies to understand how heritable genetic information of diverse organisms functions in health and disease. Provides research facilities, service cores, and staff for genomics research and training. Core facilities for Bioinformatics,DNA Technologies and Expression Analysis, Metabolomics, Proteomics,TILLING Core,Yeast One Hybrid Services Core.

Proper citation: UC Davis Genome Center Labs and Facilities (RRID:SCR_012480) Copy   

•   Source: SciCrunch Registry