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https://github.com/Cai-Lab-at-University-of-Michigan/nTracer

Software tool as plug-in for ImageJ software. Used for tracing microscopic images.

Proper citation: nTracer (RRID:SCR_023032) Copy   

•   Source: SciCrunch Registry

https://github.com/compbiolabucf/APA-Scan

Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.

Proper citation: APA-Scan (RRID:SCR_022974) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/chea3/

Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries.

Proper citation: ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) Copy   

•   Source: SciCrunch Registry

https://www.microbej.com/

Software tool for high throughput bacterial cell detection and quantitative analysis. Used to analyze bacterial cells. Used to process images derived from variety of microscopy experiments with special emphasis on large image sets. Performs intensity and morphology measurements as well as customized detection of poles, septa, fluorescent foci, and organelles, determines their sub-cellular localization with sub-pixel resolution, and tracks them over time.

Proper citation: MicrobeJ (RRID:SCR_023914) Copy   

•   Source: SciCrunch Registry

https://kleintools.hms.harvard.edu/tools/spring.html

Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data.

Proper citation: SPRING (RRID:SCR_023578) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/kea3

Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations.

Proper citation: Kinase Enrichment Analysis 3 (RRID:SCR_023623) Copy   

•   Source: SciCrunch Registry

https://github.com/SciKnowEngine/kefed.io

Knowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable.

Proper citation: Knowledge Engineering from Experimental Design (RRID:SCR_001238) Copy   

•   Source: SciCrunch Registry

http://mind.loni.usc.edu

The MiND: Metadata in NIfTI for DWI framework enables data sharing and software interoperability for diffusion-weighted MRI. This site provides specification details, tools, and examples of the MiND mechanism for representing important metadata for DWI data sets at various stages of post-processing. MiND framework provides a practical solution to the problem of interoperability between DWI analysis tools, and it effectively expands the analysis options available to end users. To assist both users and developers in working with MiND-formatted files, we provide a number of software tools for download. * MiNDHeader A utility for inspecting MiND-extended files. * I/O Libraries Programming libraries to simplify writing and parsing MiND-formatted data. * Sample Files Example files for each MiND schema. * DIRAC LONI''s Diffusion Imaging Reconstruction and Analysis Collection is a DWI processing suite which utilizes the MiND framework.

Proper citation: LONI MiND (RRID:SCR_004820) Copy   

•   Source: SciCrunch Registry

http://zfishbook.org/

Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates.

Proper citation: zfishbook (RRID:SCR_006896) Copy   

•   Source: SciCrunch Registry

http://brainmap.wisc.edu/monkey.html

NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL.

Proper citation: Rhesus Macaque Atlases for Functional and Structural Imaging Studies (RRID:SCR_008650) Copy   

•   Source: SciCrunch Registry

http://probalign.njit.edu/probalign/login

Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.

Proper citation: eProbalign (RRID:SCR_013247) Copy   

•   Source: SciCrunch Registry

https://hdpm.biomedinfolab.com/netmage/

Web tool for automated generation of interactive disease-disease network visualizations given input PheWAS summary data. Given genetic associations from Phenome-Wide Association Study, disease-disease network can be constructed where nodes represent phenotypes and edges represent shared genetic associations between phenotypes.

Proper citation: NETMAGE (RRID:SCR_021843) Copy   

•   Source: SciCrunch Registry

https://www.glygen.org

Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression.

Proper citation: GlyGen (RRID:SCR_023438) Copy   

•   Source: SciCrunch Registry

https://mibig.secondarymetabolites.org/

MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters.

Proper citation: Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) Copy   

•   Source: SciCrunch Registry

http://hanalyzer.sourceforge.net/

An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download.

Proper citation: Hanalyzer (RRID:SCR_000923) Copy   

•   Source: SciCrunch Registry

http://mus.well.ox.ac.uk/gscandb/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database / display tool of genome scans, with a web interface that lets the user view the data. It does not perform any analyses - these must be done by other software, and the results uploaded into it. The basic features of GSCANDB are: * Parallel viewing of scans for multiple phenotypes. * Parallel analyses of the same scan data. * Genome-wide views of genome scans * Chromosomal region views, with zooming * Gene and SNP Annotation is shown at high zoom levels * Haplotype block structure viewing * The positions of known Trait Loci can be overlayed and queried. * Links to Ensembl, MGI, NCBI, UCSC and other genome data browsers. In GSCANDB, a genome scan has a wide definition, including not only the usual statistical genetic measures of association between genetic variation at a series of loci and variation in a phenotype, but any quantitative measure that varies along the genome. This includes for example competitive genome hybridization data and some kinds of gene expression measurements.

Proper citation: WTCHG Genome Scan Viewer (RRID:SCR_001635) Copy   

•   Source: SciCrunch Registry

http://www.isi.edu/projects/bioscholar/overview

Knowledge management and engineering system software for experimental biomedical scientists permitting a single scientific worker (at the level of a graduate student or postdoctoral worker) to design, construct and manage a shared knowledge repository for a research group derived on a local store of PDF files. Usability is especially emphasized within a laboratory so that this software could provide support to experimental scientists attempting to construct a personalized representation of their own knowledge on a medium scale. The BioScholar system uses a graphical interface to create experimental designs based on the experimental variables in the system. The design is then analyzed to construct a tabular input form based on the data flow. They call this methodology "Knowledge Engineering from Experimental Design" or "KEfED". The approach is domain-independent but domain-specific modules reasoning can be constructed to generate interpretations from the observational data represented in the KEfED model. The application is available for download as platform-specific installers including Linux, Unix, Mac OS, and Windows. The installer will install an application that will run the BioScholar server. This server uses Jetty as its integrated web server.

Proper citation: Bioscholar (RRID:SCR_001380) Copy   

•   Source: SciCrunch Registry

http://www.csardock.org

Experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Some datasets are generated in house while others are collected from the literature or deposited by academic labs, national centers, and the pharmaceutical industry. For the community to improve their approaches, they need exceptional datasets to train scoring functions and develop new docking algorithms. They aim to provide the highest quality data for a diverse collection of proteins and small molecule ligands. They need input from the community in developing target priorities. Ideal targets will have many high-quality crystal structures (apo and 10-20 bound to diverse ligands) and affinity data for 25 compounds that range in size, scaffold, and logP. It is best if the ligand set has several congeneric series that span a broad range of affinity, with low nanomolar to mid-micromolar being most desirable. They prefer Kd data over Ki data over IC50 data (no % activity data). They will determine solubility, pKa, logP/logD data for the ligands whenever possible. They have augmented some donated IC50 data by determining Kon/Koff and ITC data.

Proper citation: Community Structure-Activity Resource (RRID:SCR_002206) Copy   

•   Source: SciCrunch Registry

https://simtk.org

A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.

Proper citation: Simtk.org (RRID:SCR_002680) Copy   

•   Source: SciCrunch Registry

http://bioportal.bioontology.org/

Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.

Proper citation: BioPortal (RRID:SCR_002713) Copy   

•   Source: SciCrunch Registry