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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | software application, data processing software, data analysis software, software resource | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-02-15 09:21:06 | 3702 | |||||
|
CVODE Resource Report Resource Website 50+ mentions |
CVODE (RRID:SCR_014696) | software application, data processing software, data analysis software, software resource | Solver for stiff and nonstiff ordinary differential equation (ODE) systems (initial value problem), given in explicit form y' = f(t,y), based on Adams and BDF methods. It is one of the programs that makes up the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis software, solver, equation solver, ordinary differential equation, differential equation, stiff, nonstiff | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014696 | SUNDIALS CVODE | 2026-02-15 09:21:01 | 56 | |||||||||
|
CalcuSyn Resource Report Resource Website 50+ mentions |
CalcuSyn (RRID:SCR_020251) | software application, data processing software, data analysis software, software resource | 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. | Biosoft, drug mixtures study, drug efficacy, dose effect, quantify synergism, quantify inhibition | is listed by: SoftCite | Restricted | SCR_020251 | CalcuSyn Version 2.0 | 2026-02-15 09:21:53 | 57 | |||||||||
|
Flowlogic Resource Report Resource Website 50+ mentions |
Flowlogic (RRID:SCR_020942) | software application, data processing software, data analysis software, software resource | Software tool for flow cytometry data analysis by Miltenyi Biotec. | Flow cytometry data, data analysis, flow cytometry, Miltenyi Biotec | is listed by: SoftCite | Restricted | SCR_020942 | Flowlogic TM Software, Flowlogic Software | 2026-02-15 09:22:27 | 74 | |||||||||
|
GRADEpro Resource Report Resource Website 100+ mentions |
GRADEpro (RRID:SCR_021308) | data management software, software application, software resource | 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. | Summary of findings tables, cochrane systematic reviews, research evidence creating, research evidence management, research evidence sharing summaries, evidence profiles, | is listed by: SoftCite | Restricted | https://cebgrade.mcmaster.ca/gradepro.html | SCR_021308 | Guideline Development Tool, GRADEpro GDT, GDT, GRADE Guideline Development Tool, G2DT | 2026-02-15 09:22:32 | 376 | ||||||||
|
jcvi Resource Report Resource Website 10+ mentions |
jcvi (RRID:SCR_021641) | software library, software toolkit, software resource | Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. | Python libraries, parse bioinformatics files, assembly, annotation, comparative genomics | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/tanghaibao/jcvi/tree/v0.5.7 https://zenodo.org/record/31631#.YRaieYhKhPa |
SCR_021641 | jcvi_PyPI, jcvi 1.1.17 | 2026-02-15 09:22:33 | 15 | ||||||||
|
SEDFIT Resource Report Resource Website 10+ mentions |
SEDFIT (RRID:SCR_018365) | software application, data processing software, data analysis software, software resource | Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly. | Analytical ultracentrifugation, biophysical analysis, macromolecular assembly, data, analysis, National Institute of Biomedical Imaging and Bioengineering | is listed by: SoftCite | NIH | Free, Available for download, Freely available | SCR_018365 | SEDFIT version 14.7g | 2026-02-15 09:22:21 | 25 | ||||||||
|
PRISMA Resource Report Resource Website 1000+ mentions |
PRISMA (RRID:SCR_018721) | PRISMA | data or information resource, narrative resource, standard specification, portal | Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions. | MDAR, standard, report standard, reporting reviews, randomized trial, evaluating randomized trial, reporting systematic review, intervention evaluation, meta analysis | is listed by: SoftCite | Ottawa Hospital Research Institute ; University of Oxford |
Free, Freely available | SCR_018721 | Preferred Reporting Items for Systematic Reviews and Meta-Analyses | 2026-02-15 09:22:16 | 1069 | |||||||
|
Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | software application, data processing software, data analysis software, software resource | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | 2026-02-15 09:22:16 | 42 | ||||||
|
ELDA Resource Report Resource Website 100+ mentions |
ELDA (RRID:SCR_018933) | software application, data processing software, software resource, service resource, production service resource, analysis service resource, data analysis software | Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly. | Limiting dilution analysis, stem cell assay, data set confidence intervals, single hit hypothesis, adequacy test, frequency differences test | is listed by: SoftCite | PMID:19567251 | Free, Freely available | SCR_018933 | Extreme Limiting Dilution Analysis | 2026-02-15 09:22:25 | 385 | ||||||||
|
PROCHECK Resource Report Resource Website 50+ mentions |
PROCHECK (RRID:SCR_019043) | software application, data processing software, data analysis software, software resource | Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR. | Stereochemical quality, protein structure, plot, residue listing, protein, assessing protein quality, | is listed by: SoftCite | DOI:10.1107/S0021889892009944 | Free, Available for download | SCR_019043 | 2026-02-15 09:22:21 | 75 | |||||||||
|
igraph Resource Report Resource Website 100+ mentions |
igraph (RRID:SCR_019225) | software application, data visualization software, data processing software, software resource, network graph visualization software, network analysis software, software toolkit, data analysis software | Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus. | Graphs analysis, network analysis, generating graph function, graph visualization |
is listed by: CRAN is listed by: SoftCite is related to: igraph for R |
Free, Available for download, Freely available | https://igraph.org/ https://github.com/igraph/igraph/releases/tag/0.8.4 |
SCR_019225 | igraph 0.8.4, igraph 1.2.6 | 2026-02-15 09:22:21 | 354 | ||||||||
|
OpenClinica Resource Report Resource Website 10+ mentions |
OpenClinica (RRID:SCR_019223) | software application, data processing software, data acquisition software, software resource | Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system. | Clinical trial, data management system, clinical trial management system, clinical data, clinical data management | is listed by: SoftCite | PMID:21893916 | Restricted | https://www.openclinica.com/community-edition-open-source-edc/ | SCR_019223 | 2026-02-15 09:22:28 | 35 | ||||||||
|
FCS Express Resource Report Resource Website 100+ mentions |
FCS Express (RRID:SCR_016431) | software application, data processing software, data analysis software, software resource | Software tool for flow and image cytometry data analysis by De Novo Software company. | flow, image, analysis, data, cytometry, De Novo Software, research, clinical, laboratory | is listed by: SoftCite | Commercially available, Tutorial available | SCR_016431 | 2026-02-15 09:21:52 | 488 | ||||||||||
|
EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | software application, image processing software, data processing software, software resource | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | EMAN1, EMAN2 | 2026-02-15 09:21:55 | 106 | |||
|
BLASTClust Resource Report Resource Website 50+ mentions |
BLASTClust (RRID:SCR_016641) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets. | cluster, protein, nucleotide, sequence, pairwise, match, sequence |
is listed by: SoftCite has parent organization: NCBI works with: NCBI BLAST |
Free, Freely available | SCR_016641 | 2026-02-15 09:21:46 | 88 | ||||||||||
|
CTFFIND Resource Report Resource Website 100+ mentions |
CTFFIND (RRID:SCR_016732) | CTFFIND | software application, data processing software, data analysis software, software resource | Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4. |
is listed by: SoftCite is related to: Janelia Research has parent organization: MRC Laboratory of Molecular Biology |
MRC | PMID:26278980 | SCR_016732 | CTFFinding, CTFFIND4, CTFFIND2, Contrast Transfer Function Finding, Contrast Transfer FunctionFinding, CTFFIND 3 | 2026-02-15 09:21:48 | 109 | ||||||||
|
RNAstructure Resource Report Resource Website 10+ mentions |
RNAstructure (RRID:SCR_017216) | software application, software resource, data access protocol, web service, service resource, production service resource, simulation software, analysis service resource | Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program. | RNA, DNA, secondary, structure, prediction, analysis |
is listed by: SoftCite has parent organization: University of Rochester; New York; USA |
NIGMS R01 GM076485 | PMID:23620284 | Free, Freely available | SCR_017216 | 2026-02-15 09:21:59 | 42 | ||||||||
|
CFX Manager Resource Report Resource Website 100+ mentions |
CFX Manager (RRID:SCR_017251) | software application, data processing software, data analysis software, software resource | Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | RT PCR, real time PCR, data, analysis, BioRad | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017251 | CFX Manager software | 2026-02-15 09:22:00 | 489 | |||||||||
|
ClustalW Resource Report Resource Website 10000+ mentions |
ClustalW (RRID:SCR_017277) | ClustalW of DDBJ | web service, data access protocol, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.Web sevice of ClustalW provided by DNA data bank of Japan. | alignment, service, DNA, data, bank, Japan | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017277 | ClustalW of DNA Data Bank of Japan | 2026-02-15 09:21:18 | 10543 |
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