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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NEST Simulator Resource Report Resource Website 100+ mentions |
NEST Simulator (RRID:SCR_002963) | NEST | software application, simulation software, software resource | Software tool as simulator for spiking neural network models that focuses on dynamics, size and structure of neural systems rather than on exact morphology of individual neurons. Used for any size spiking neurons networks including models of information processing, models of network activity dynamics, models of learning and plasticity. | simulation, neuron, spiking, neural network, model, neural system, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: MUlti SImulation Coordinator has parent organization: NEST Initiative |
DOI:10.1007/978-1-4614-7320-6_258-5 | Free, Available for download, Freely available | nif-0000-00162, biotools:nest | https://github.com/nest/nest-simulator, https://bio.tools/nest | SCR_002963 | Neural Simulation Tool, NEural Simulation Tool, nest, nest-simulator | 2026-08-05 10:43:43 | 175 | |||||
|
HCLUST Resource Report Resource Website 1000+ mentions |
HCLUST (RRID:SCR_009154) | HCLUST | software application, software resource | Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:h-clust, SCR_009102, nlx_154195, nlx_154331 | https://bio.tools/h-clust | SCR_009154 | R/HCLUST | 2026-08-05 10:45:12 | 1459 | ||||||
|
PyBEL Resource Report Resource Website 1+ mentions |
PyBEL (RRID:SCR_017660) | software toolkit, software resource | Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J. | Parsing, validating, compiling, converting, network, BEL, biological, expression, language, bio.tools |
is used by: Bio2BEL is listed by: bio.tools is listed by: Debian is related to: Biological Expression Language |
European Union/European Federation of Pharmaceutical Industries and Associations (EFPIA) Innovative Medicines Initiative Joint Undertaking | PMID:29048466 | Free, Available for download, Freely available | biotools:pybel, SCR_024180 | https://github.com/pybel/pybel, https://bio.tools/pybel/, https://pybel.readthedocs.io | https://sources.debian.org/src/python3-pybel/ | SCR_017660 | pybel, Python Biological Expression Language | 2026-08-05 10:46:50 | 1 | ||||
|
kempbasu Resource Report Resource Website |
kempbasu (RRID:SCR_024055) | software toolkit, software resource | Software package implements two significance tests for comparing digital gene expression profiles. They provide two programs: Kemp for the frequentist test and Basu for the Bayesian test, and some auxiliary scripts. | comparing digital gene expression profiles, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/kempbasu/ | SCR_024055 | 2026-08-05 10:47:57 | 0 | |||||||||
|
BioImageXD Resource Report Resource Website 10+ mentions |
BioImageXD (RRID:SCR_023979) | software toolkit, software resource | Software package for analyzing, processing and visualizing multi-dimensional microscopy images. Multipurpose postprocessing tool for bioimaging. Can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once. | post-processing tool, bioimaging, visualization, multi-channel temporal image stacks, 3D rendering of multiple channels at once, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bioimagexd/ | SCR_023979 | bioimagexd | 2026-08-05 10:47:56 | 25 | ||||||||
|
BAli-Phy Resource Report Resource Website |
BAli-Phy (RRID:SCR_023976) | software application, source code, software resource | Software application as simultaneous Bayesian inference of alignment and phylogeny. Used to estimate multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. to explore the joint space of alignment and phylogeny given molecular sequence data. BAli-Phy version 3 is model based co-estimation of alignment and phylogeny. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. Implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously. | estimate multiple sequence alignments, estimate evolutionary trees, DNA sequences, amino acid sequences, codon sequences, | is listed by: Debian | PMID:16679334 PMID:33677478 |
Free, Available for download, Freely available | OMICS_03734 | https://sources.debian.org/src/bali-phy/ | SCR_023976 | bali-phy, BAli-Phy version 3 | 2026-08-05 10:47:56 | 0 | ||||||
|
Intake Resource Report Resource Website |
Intake (RRID:SCR_024042) | software toolkit, software resource | Software package for finding, investigating, loading and disseminating data. | finding data, investigating data, loading data, disseminating data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/intake/, https://intake.readthedocs.io/en/latest/ | SCR_024042 | Intake: A general interface for loading data, intake | 2026-08-05 10:47:57 | 0 | ||||||||
|
iVar Resource Report Resource Website 50+ mentions |
iVar (RRID:SCR_024045) | software toolkit, software resource | Software package for viral amplicon based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.Contains intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.Following functions are implemented in iVar: trimming of primers and low-quality bases; consensus calling; variant calling both iSNVs and insertions/deletions; identifying mismatches to primer sequences and excluding the corresponding reads from alignment files. | call iSNVs from viral sequencing data, viral amplicon based sequencing, call iSNVs and consensus sequences from viral sequencing data, call iSNVs | is listed by: Debian | PMID:30621750 | Free, Available for download, Freely available, | https://sources.debian.org/src/ivar/, https://andersen-lab.github.io/ivar/html/ | SCR_024045 | ivar | 2026-08-05 10:47:57 | 66 | |||||||
|
Change-O Resource Report Resource Website 1+ mentions |
Change-O (RRID:SCR_023986) | software toolkit, software resource | Collection of software tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, and reconstructing germline sequences. | processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, reconstructing germline sequences, | is listed by: Debian | PMID:26069265 | Free, Available for download, Freely available | OMICS_08874 | https://sources.debian.org/src/changeo/ | SCR_023986 | changeo | 2026-08-05 10:47:56 | 9 | ||||||
|
GATB Resource Report Resource Website 1+ mentions |
GATB (RRID:SCR_024024) | software toolkit, software resource | Software genome analysis toolbox with de-Bruijn graph. Library dedicated to genome assembly and analysis. | genome assembly, genome analysis, | is listed by: Debian | PMID:24990603 | Free, Available for download, Freely available | OMICS_04834 | https://sources.debian.org/src/gatb-core/, https://gatb.inria.fr/software/gatb-core/ | SCR_024024 | GATB-CORE, gatb-core, GATB-TOOLS, The Genome Analysis Toolbox with de-Bruijn graph | 2026-08-05 10:47:57 | 3 | ||||||
|
bambamc Resource Report Resource Website |
bambamc (RRID:SCR_023970) | software toolkit, software resource | Software package contains lightweight C implementation of name collating BAM file input and BAM file output. | C implementation, name collating BAM file input, BAM file output, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bambamc/ | SCR_023970 | 2026-08-05 10:47:56 | 0 | |||||||||
|
bamkit Resource Report Resource Website |
bamkit (RRID:SCR_023969) | software toolkit, software resource | Software tools for common BAM file manipulations. | BAM file manipulations, BAM file, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bamkit/ | SCR_023969 | 2026-08-05 10:47:56 | 0 | |||||||||
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Atropos Resource Report Resource Website 1+ mentions |
Atropos (RRID:SCR_023962) | software application, source code, software resource | Software tool for specific, sensitive, and speedy trimming of NGS reads. | speedy trimming of NGS reads, NGS reads, Next Generation Sequencing, | is listed by: Debian | PMID:28875074 | Free, Available for download, Freely available | OMICS_20869 | https://sources.debian.org/src/atropos/ | SCR_023962 | atropos | 2026-08-05 10:47:56 | 3 | ||||||
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FAST Analysis of Sequences Toolbox Resource Report Resource Website |
FAST Analysis of Sequences Toolbox (RRID:SCR_024074) | FAST | software toolkit, software resource | Software Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records.FAST workflows are designed for serial processing of flatfile biological sequence record databases per-sequence, rather than per-line, through UNIX pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FASTQ format is supported. FAST is designed for learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, and reproducibility. FAST tools expose the power of Perl and BioPerl to users in an easy-to-learn command-line paradigm. | Analysis of sequences, UNIX utilities, UNIX toolbox paradigm to bioinformatic sequence records, serial processing, flatfile biological sequence record databases per-sequence, FASTQ format, learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, reproducibility | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libfast-perl/ | SCR_024074 | libfast-perl, Fast Analysis of Sequences Toolbox, FAST - FAST Analysis of Sequences Toolbox, fast | 2026-08-05 10:47:57 | 0 | |||||||
|
Bio-PrimerDesigner Resource Report Resource Website |
Bio-PrimerDesigner (RRID:SCR_024082) | software toolkit, software resource | Software package provides low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio-PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported. | interface to the primer3 and epcr binary executables, methods to return the results, accessing primer3 binary via remote server, Unix hosts supported, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-primerdesigner-perl/ | SCR_024082 | Bio-PrimerDesigner - Design PCR Primers using primer3 and epcr, libbio-primerdesigner-perl | 2026-08-05 10:47:58 | 0 | ||||||||
|
rasmol Resource Report Resource Website 10+ mentions |
rasmol (RRID:SCR_024208) | software toolkit, software resource | Software package for molecular graphics visualisation.Used for visualisation of molecules. | biomolecular graphics, molecules visualisation, | is listed by: Debian | PMID:7482707 | Free, Available for download, Freely available, | OMICS_05076 | https://sources.debian.org/src/rasmol/ | SCR_024208 | RasMol | 2026-08-05 10:48:00 | 13 | ||||||
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Raster3D Resource Report Resource Website |
Raster3D (RRID:SCR_024220) | software toolkit, software resource | Software tools for generating high quality raster images of proteins or other molecules. Photorealistic molecular graphics. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. | generating high quality raster images, protein images, molecules images, images generation, molecular graphics, | is listed by: Debian | PMID:18488322 | Free, Available for download, Freely available, | OMICS_05054 | https://sources.debian.org/src/raster3d/ | SCR_024220 | raster3d | 2026-08-05 10:48:00 | 0 | ||||||
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Biobase Resource Report Resource Website 10+ mentions |
Biobase (RRID:SCR_024224) | software toolkit, software resource | Software R package provides functions that are needed by many other packages or which replace R functions. Base functions for Bioconductor. | Base functions for Bioconductor, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-biobase/ | SCR_024224 | 2026-08-05 10:48:01 | 28 | |||||||||
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fitbitscraper Resource Report Resource Website |
fitbitscraper (RRID:SCR_024273) | software toolkit, software resource | Software R package to scrape data from Fitbit to generate graphs. | generate graphs, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-fitbitscraper/ | SCR_024273 | 2026-08-05 10:48:01 | 0 | |||||||||
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fitdistrplus Resource Report Resource Website 1+ mentions |
fitdistrplus (RRID:SCR_024274) | software toolkit, software resource | Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data. | extend fitdistr function, parametric distribution fit, non-censored or censored data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-fitdistrplus/ | SCR_024274 | 2026-08-05 10:48:01 | 1 |
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