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https://www.iconplc.com/innovation/nonmem/
Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions.
Proper citation: NONMEM (RRID:SCR_016986) Copy
http://www.cbs.dtu.dk/services/SignalP/
Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
Proper citation: SignalP (RRID:SCR_015644) Copy
Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
http://quantprime.mpimp-golm.mpg.de
Fully automated tool for primer pair design in small- to large-scale real-time reverse transcription qPCR analyses. It offers design and specificity checking with highly customizable parameters and is available for use with publicly available eukaryotic transcriptomes.
Proper citation: QuantPrime (RRID:SCR_015498) Copy
http://www.vsh.com/products/mflt/index.asp
Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software.
Proper citation: ModFit LT (RRID:SCR_016106) Copy
https://www.miltenyibiotec.com/products/macs-flow-cytometry/software/flowlogic-software.html
Software tool for flow cytometry data analysis by Miltenyi Biotec.
Proper citation: Flowlogic (RRID:SCR_020942) Copy
Software tool used to create summary of findings tables for cochrane systematic reviews. Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables.
Proper citation: GRADEpro (RRID:SCR_021308) Copy
https://pypi.org/project/jcvi/
Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
Proper citation: jcvi (RRID:SCR_021641) Copy
http://www.biosoft.com/w/calcusyn.htm
Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools.
Proper citation: CalcuSyn (RRID:SCR_020251) Copy
A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MutationAssessor (RRID:SCR_005762) Copy
http://bioapps.rit.albany.edu/MITOPRED/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It predicts nuclear-encoded mitochondrial proteins from all eukaryotic species including plants. Prediction is based on the occurrence patterns of Pfam domains (version 16.0) in different cellular locations, amino acid composition and pI value differences between mitochondrial and non-mitochondrial locations. Additionally, you may download MITOPRED predictions for complete proteomes. Re-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. The Mitopred algorithm works based on the differences in the Pfam domain occurrence patters and amino acid composition differences in different cellular compartments. Location specific Pfam domains have been determined from the entire eukaryotic set of Swissprot database. Similarly, differences in the amino acid composition between mitochondrial and non-mitochondrial sequences were pre-calculated. This information is used to calculate location-specific amino acid weights that are used to calculate amino acid score. Similarly, pI average values of the N-terminal 25 residues in different cellular location were also determined. This knowledge-base is accessed by the program during execution.
Proper citation: mitopred (RRID:SCR_006135) Copy
A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions.
Proper citation: GBrowse (RRID:SCR_006829) Copy
http://www.ncbi.nlm.nih.gov/tools/primer-blast/
A tool to design target-specific primers for polymerase chain reaction (PCR). It uses Primer3 to design PCR primers and then uses BLAST and global alignment algorithm to screen primers against user-selected database in order to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause non-specific amplifications.
Proper citation: Primer-BLAST (RRID:SCR_003095) Copy
A commercial software tool for statistical analysis.
Proper citation: SyStat (RRID:SCR_010455) Copy
Powerful, accessible statistical tools for fast visualization and analysis of microarrays - expression arrays, miRNA, exon arrays and genomics copy number data.
Proper citation: GeneSpring GX (RRID:SCR_010972) Copy
http://www.perkinelmer.com/pages/020/cellularimaging/products/openlab.xhtml
A software package for performing 2D microscope image processing and integrating and controlling a diverse array of instrumentation in a laboratory environment. The software suite has four basic areas of operation acquisition, image presentation, and storage, analysis, and automation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Openlab (RRID:SCR_012158) Copy
http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV/
Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins.
Proper citation: MetaPSICOV (RRID:SCR_024517) Copy
A web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals. It compiles all the possible clusters of piRNAs and also depicts piRNAs along with the associated genomic elements like genes and repeats on a genome wide map. piRNABank mainly provides data onnamely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila.Search options have been designed to query and obtain useful data from this online resource. It also facilitates abstraction of sequences and structural features from piRNA data. piRNABank provides the following features: * Simple search * Search piRNA clusters * Search homologous piRNAs * piRNA visualization map * Analysis tools, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: piRNABank (RRID:SCR_007858) Copy
Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results.
Proper citation: Gemma (RRID:SCR_008007) Copy
A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base .
Proper citation: Ingenuity Pathways Knowledge Base (RRID:SCR_008117) Copy
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