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https://www.thermofisher.com/us/en/home/industrial/spectroscopy-elemental-isotope-analysis/molecular-spectroscopy/fluorometers/qubit/qubit-fluorometer.html

Benchtop fluorometer designed to accurately measure DNA, RNA, and protein quantity. Measures RNA integrity and quality. Touch screen to select and run assays with results displayed in few seconds.

Proper citation: Thermo Fisher Qubit fluorimeter (RRID:SCR_018095) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/nsegata/phylophlan/wiki/Home

Software pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. Pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PhyloPhlAn (RRID:SCR_013082) Copy   

•   Source: SciCrunch Registry

http://homes.gersteinlab.org/Khurana-PLoSCompBio-2013/

Software for an integrated network combining multiple biological network database sources into a single human protein interactome. The software package contains gene interaction pairs corresponding to the unified global network.

Proper citation: MultiNet (RRID:SCR_016149) Copy   

•   Source: SciCrunch Registry

http://www.capitalbiosciences.com/

Biological products including Cell Immortalization Products, Clinically Defined Human Tissue, cDNA ORF Clones, Premade Adenoviruses, Purified Proteins, Viral Expression Systems and others as well as services like Custom Recombinant Adenovirus Production, Custom Recombinant Lentivirus Production, Protein Detection and Quantification and Stable Cell Line Production for academic and governmental research institutes, pharmaceutical and biotechnology industry. Capital Biosciences offers most types of human tissues, normal and diseased, with extensive clinical history and follow up information. Standard specimen format: Snap-frozen(flash-frozen), Formalin fixed and paraffin embedded (FFPE) tissues, Blood and blood products, Bone marrow, Total RNA, Genomic DNA, Total Proteins, Primary cell cultures, Viable frozen tissue. Tumor tissue samples include: Bladder cancer, Glioblastoma, Medulloblastoma, Breast Carcinoma, Cervical Cancer, Colorectal Cancer, Endometrial Cancer, Esophageal Cancer, Head and Neck (H&N) Carcinoma, Hepatocellular Carcinoma (HCC), Hodgkin's lymphoma, Kidney, Renal Cell Carcinoma, Lung Cancer, Non-Small Cell (NCSLC), Lung Cancer, Small Cell (SCLC), Melanoma, Mesothelioma, non-Hodgkin's Lymphoma, Ovarian Adenocarcinoma, Pancreatic Cancer, Prostate Cancer, Stomach Cancer.

Proper citation: Capital Biosciences (RRID:SCR_004879) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Rebholz-srv/ebimed/

A web application that combines Information Retrieval and Extraction from Medline. EBIMed finds Medline abstracts in the same way PubMed does. Then it goes a step beyond and analyses them to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species. The results are shown in a table that displays all the associations and links to the sentences that support them and to the original abstracts. By selecting relevant sentences and highlighting the biomedical terminology EBIMed enhances your ability to acquire knowledge, relate facts, discover implications and, overall, have a good overview economizing the effort in reading.

Proper citation: EBIMed (RRID:SCR_005314) Copy   

•   Source: SciCrunch Registry

http://www.gramene.org

Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

Proper citation: Gramene (RRID:SCR_002829) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/orfer/

An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number.

Proper citation: ORFprimer (RRID:SCR_003269) Copy   

•   Source: SciCrunch Registry

http://www.rockland-inc.com/

A global biotechnology company manufacturing research tools, antibodies, and cGMP grade protein.

Proper citation: Rockland Immunochemicals (RRID:SCR_003278) Copy   

•   Source: SciCrunch Registry

http://nrresource.org

Collection of individual databases on members of the steroid and thyroid hormone receptor superfamily. Although the databases are located on different servers and are managed individually, they each form a node of the NRR. The NRR itself integrates the separate databases and allows an interactive forum for the dissemination of information about the superfamily. NRR Components: Androgen receptor, Estrogen receptor, Glucocorticoid receptor, Peroxisome proliferator, Steroid receptor protein, Thyroid receptor, Vitamin D receptor.

Proper citation: Nuclear Receptor Resource (RRID:SCR_003285) Copy   

•   Source: SciCrunch Registry

http://www.ensembl.org/

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Proper citation: Ensembl (RRID:SCR_002344) Copy   

•   Source: SciCrunch Registry

http://www.abazyme.com/

Commercial antibody supplier that provides reagents such as immunoassay kits, antibodies, and proteins as well as custom services such as antigen preparation, sequencing and engineering.

Proper citation: Abazyme (RRID:SCR_001139) Copy   

•   Source: SciCrunch Registry

https://atlasantibodies.com/

An antibody supply company that provides reagents targeting all human proteins. Atlas Antibodies develops reagents and antibodies for mass-spectrometry-based quantitative proteomics as well. Their production and development is based on the Human Protein Atlas (HPA) project, which released a complete tissue-based map of human protein expression using antibodies.

Proper citation: Atlas Antibodies (RRID:SCR_001137) Copy   

•   Source: SciCrunch Registry

http://iclab.life.nctu.edu.tw/iclab_webtools/sodock/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems.

Proper citation: SODOCK (RRID:SCR_000193) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/as-peak/

A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.

Proper citation: AS-Peak (RRID:SCR_000380) Copy   

•   Source: SciCrunch Registry

http://thomsonreuters.com/metadrug/

A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization

Proper citation: MetaDrug (RRID:SCR_000461) Copy   

•   Source: SciCrunch Registry

http://expasy.org/

Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. It contains resources from many different SIB groups as well as external institutions.

Proper citation: ExPASy Bioinformatics Resource Portal (RRID:SCR_012880) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/research-and-faculty/resources/optogenetics-resource

Mouse lines expressing proteins that activate, inhibit or detect neuronal activity are available from The Jackson Laboratory Repository. Many of these strains have been generated by HHMI Janelia Farm GENIE Project or by Allen Institute for Brain Science.

Proper citation: Optogenetics Resource at JAX (RRID:SCR_017508) Copy   

•   Source: SciCrunch Registry

http://as-alps.nagahama-i-bio.ac.jp

This database, AS-ALPS (Alternative Splicing-induced ALteration of Protein Structure), is aimed at providing useful information to analyze effect of AS on protein interaction and network through alteration of protein structure. In AS-ALPS, regions of amino acid sequences changed by AS (AS regions) which are detected in human and mouse transcript sequences in H-InvDB, FANTOM and RefSeq, are linked to information extracted from PDB about residues forming hydrophobic cores and inter-molecular interaction sites. This makes it possible to directly infer whether protein structure and/or interaction are affected by each AS event. In addition, AS-ALPS provides links to a protein network database KEGG, making it easy to know which network and which node in the network can be influenced by AS. :Sponsors: This database was supported by a grant of the Genome Network Project from Ministry of Education, Culture, Sports, Science and Technology of Japan. :

Proper citation: Alternate Splicing - induced ALteration of Protein Structure (RRID:SCR_007554) Copy   

•   Source: SciCrunch Registry

http://blocks.fhcrc.org

Blocks is a database of highly conserved regions of proteins, or Blocks. THe database is no longer maintained or updated and some of its tools are no longer functional. However, Blocks does provide Block Searcher, Get Blocks and Block Maker, aids to detection and verification of protein sequence homology. They compare a protein or DNA sequence to a database of protein blocks (current version), retrieve blocks, and create new blocks, respectively. Users can further view blocks by (keyword or number), search a sequence against the database of blocks, search blocks against each other, or make blocks of their own.

Proper citation: Blocks (RRID:SCR_007567) Copy   

•   Source: SciCrunch Registry

http://pir.georgetown.edu/iprolink/biothesaurus

BioThesaurus is a web-based system designed to map a comprehensive collection of protein and gene names to UniProt Knowledgebase protein entries. It covers all UniProtKB protein entries, and consists of several millions of names extracted from multiple resources based on database cross-references in iProClass. The web site allows the retrieval of synonymous names of given protein entries and the identification of ambiguous names shared by multiple proteins. Searches can be done on protein/gene name, organism, or unique identifier.

Proper citation: BioThesaurus (RRID:SCR_007566) Copy   

•   Source: SciCrunch Registry