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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BRAHMS Resource Report Resource Website 10+ mentions |
BRAHMS (RRID:SCR_015642) | software resource | Simulation software that runs network simulations where the network is specified in its own format called SystemML. The components of the network can be implemented in C, C++, Python or Matlab and are used in SpineML_2_BRAHMS to provide a simulation back-end for SpineML models. | neural network, simulation, modeling software, spineml, systemml, c, c++, python, matlab | is used by: SpineML_2_BRAHMS | DOI:10.1016/j.aei.2009.08.002 | Free, Available for download | http://brahms.sourceforge.net/home/ | SCR_015642 | 2026-08-08 12:00:24 | 19 | ||||||||
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Phobius Resource Report Resource Website 500+ mentions |
Phobius (RRID:SCR_015643) | production service resource, web service, software resource, data access protocol, analysis service resource, service resource | Web application for combined transmembrane topology and signal peptide prediction. Used for whole genome annotation of signal peptides and transmembrane regions. Predictor is based on hidden Markov model (HMM) that models different sequence regions of signal peptide and different regions of transmembrane protein in series of interconnected states. | Signal peptide prediction, whole genome annotation, transmembrane region, protein prediction, transmembrane topology, signal peptide, fasta, hidden markov model | is listed by: SoftCite | PMID:15111065 PMID:30976793 |
Freely Available, Free, Available for download | SCR_018767 | http://phobius.binf.ku.dk/, https://www.ebi.ac.uk/Tools/pfa/phobius/ | SCR_015643 | PHOBIUS | 2026-08-08 12:00:38 | 553 | ||||||
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HISAT2 Resource Report Resource Website 10000+ mentions |
HISAT2 (RRID:SCR_015530) | sequence analysis software, software resource, software application, source code, data analysis software, data processing software | Graph-based alignment of next generation sequencing reads to a population of genomes. | alignment program, mapping reads, population genomics, human genome, bio.tools |
is used by: Fcirc is listed by: Debian is listed by: bio.tools is related to: TopHat has parent organization: Johns Hopkins University; Maryland; USA is required by: SL-quant is hosted by: GitHub |
NLM R01-LM06845; NIGMS R01-GM083873; NSF CCF-0347992 |
PMID:25751142 DOI:10.1038/s41587-019-0201-4 |
Available for download | OMICS_07225, biotools:hisat2 | https://github.com/infphilo/hisat2, https://bio.tools/hisat2, https://sources.debian.org/src/hisat2/ | SCR_015530 | HISAT | 2026-08-08 12:00:41 | 20753 | |||||
|
Platanus Resource Report Resource Website 100+ mentions |
Platanus (RRID:SCR_015531) | sequence analysis software, software resource, software application, data analysis software, data processing software | De novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | de novo sequence assembly, genomic sequence reconstruction, shotgun sequence data | DOI:10.1101/gr.170720.113 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015531 | PLATform for Assembling NUcleotide Sequences, Platanus - PLATform for Assembling NUcleotide Sequences, Platanus Genome Assembler | 2026-08-08 12:00:24 | 201 | |||||||||
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Elastica2D Resource Report Resource Website 1+ mentions |
Elastica2D (RRID:SCR_015858) | data or information resource, model, software resource, software application, data visualization software, data processing software | Software for a 2D elastic beam model that can be used to model quasistatic bending of the vibrissa to compute forces and bending moments at the base. Elastica2D is part of the Digital Rat software project that that aims to enable morphologically and mechanically accurate modelling of the rat head and vibrissal (whisker) array. | matlab, quasistatic bending, vibrissa, 2d model, elastic, elastic beam, mechanical model | is used by: MATLAB | National Science Foundation 0446391; National Science Foundation 0818414; National Science Foundation 0846088 |
PMID:22298834 | Free, Available for download | SCR_015858 | 2026-08-08 12:00:43 | 1 | ||||||||
|
Quantum Biology Institute Resource Report Resource Website |
Quantum Biology Institute (RRID:SCR_015855) | access service resource, service resource | Institute that provides resources and researches the concepts and mechanisms which underlie the complexities of biology. In particular, it incorporates concepts in physics and mathematics to resolve, unravel, and explain complex biological mechanisms and conditions. | physics, mathematics, quantum biology, biological mechanism | Available to the scientific community | http://www.nitrc.org/projects/foliations_2050/ | SCR_015855 | 2026-08-08 12:00:45 | 0 | ||||||||||
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Stanford Diabetes Research Center Resource Report Resource Website 1+ mentions |
Stanford Diabetes Research Center (RRID:SCR_015856) | access service resource, service resource | University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Stanford University. | stanford, diabetes, research center, niddk, service resource |
is listed by: NIDDK Information Network (dkNET) is listed by: Diabetes Research Centers has organization facet: Stanford Diabetes Research Center Diabetes Immune Monitoring Core has organization facet: Stanford Diabetes Research Center Stanford Islet Research Core has organization facet: Stanford Diabetes Research Center Diabetes Clinical and Translational Core has organization facet: Stanford Diabetes Research Center Diabetes Genomics Analysis Core is organization facet of: Diabetes Research Centers |
NIDDK P30 DK116074 | Available to the scientific community | SCR_015856 | 2026-08-08 12:00:26 | 1 | |||||||||
|
Clinical Trials in Organ Transplantation (CTOT) Resource Report Resource Website 1+ mentions |
Clinical Trials in Organ Transplantation (CTOT) (RRID:SCR_015859) | CTOT | data or information resource, consortium, project portal, portal, organization portal | Project portal for a cooperative research program to improve short and long-term graft and patient survival. CTOT is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for transplant recipients. | graft, graft patient, patient survival, clinical study, transplant, transplant recipient, mechanistic study |
is listed by: NIDDK Information Network (dkNET) is listed by: Diabetes Research Centers is related to: Clinical Trials in Organ Transplantation in Children (CTOT-C) |
NIAID UM2 AI117870 | Public, Available to the scientific community | SCR_015859 | Clinical Trials in Organ Transplantation | 2026-08-08 12:00:45 | 1 | |||||||
|
Clinical Trials in Organ Transplantation in Children (CTOT-C) Resource Report Resource Website 1+ mentions |
Clinical Trials in Organ Transplantation in Children (CTOT-C) (RRID:SCR_015860) | CTOT-C | data or information resource, consortium, project portal, portal, organization portal | Project portal for a cooperative research program sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). CTOT-C is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for pediatric heart, lung, or kidney transplant recipients. | heart, kidney, lung, pediatric, cooperative research program, niaid, clinical study, mechanistic study, transplant |
is listed by: NIDDK Information Network (dkNET) is related to: Clinical Trials in Organ Transplantation (CTOT) |
NIAID UM2 AI117870 | Public, Available to the scientific community | SCR_015860 | NIAID Clinical Trials in Organ Transplantation in Children, Clinical Trials in Organ Transplantation in Children, NIAID CTOT-C | 2026-08-08 12:00:26 | 1 | |||||||
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SpiCoDyn Resource Report Resource Website 1+ mentions |
SpiCoDyn (RRID:SCR_015744) | software resource, software application, source code, data analysis software, data processing software | Software for the analysis of multi-site neuronal spike signals. SPICODYN processes electrophysiological signals, focusing on spiking and bursting dynamics and functional-effective connectivity analysis. | spike signal, neuron, multi-site neuronal spike signal, eeg, electrophysiology, brain imaging | Open source, Available for download | SCR_015744 | 2026-08-08 12:00:25 | 2 | |||||||||||
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Hybrid-denovo Resource Report Resource Website 1+ mentions |
Hybrid-denovo (RRID:SCR_015866) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software for a de novo OTU-picking pipeline integrating single- and paired-end 16S sequence tags. It is designed to take Illumina paired-end sequencing reads as input and output the OTU BIOM table, together with their representative sequences and a phylogenetic tree of OTUs. | hybrid-denovo, 16S rRNA, microbiota pipeline, single-end, paired-end, illumina read, de novo, otu-picking pipeline, phylogenetic tree, python, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:hybrid-denovo | https://bio.tools/hybrid-denovo | SCR_015866 | 2026-08-08 12:00:43 | 3 | |||||||||
|
RNAcompete Resource Report Resource Website 1+ mentions |
RNAcompete (RRID:SCR_015900) | software resource, software application, data analysis software, data processing software | Method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. RNAcompete identifies expected and previously unknown RNA binding preferences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rna, protein, interaction, binding, preference, rna-seq, recognition, rbp, k-mer, structured rna, unstructured rna, matlab |
uses: MATLAB has parent organization: University of Toronto; Ontario; Canada |
CIHR MOP-49451; CIHR MOP-14609; CIHR MOP-93671; Natural Sciences and Engineering Research Council ; Canadian Foundation of Innovation ; Ontario Genomics Institute ; Ontario Research Fund ; National Science and Engineering Research Council of Canada (NSERC) |
PMID:19561594 PMID:27956239 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_18668 | SCR_015900 | RNAcompete Tool | 2026-08-08 12:00:27 | 1 | ||||||
|
PISA Resource Report Resource Website 1000+ mentions |
PISA (RRID:SCR_015749) | PDBePISA | web application, software resource | Web application for exploration of macromolecular interfaces. It calculates structural and chemical properties of macromolecular surfaces and interfaces, as well as quaternary structures (assemblies), their structural and chemical properties and dissociation patterns. | macromolecule, assembly, dissociation pattern, chemical composition | BBSRC 721/B19544 | PMID:17681537 | Freely available, Free, Available for download, Tutorial available | SCR_015749 | PDBePISA, Proteins Interfaces Structures and Assemblies | 2026-08-08 12:00:43 | 1638 | |||||||
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UCSF ChimeraX Resource Report Resource Website 1000+ mentions |
UCSF ChimeraX (RRID:SCR_015872) | software resource, 3d visualization software, software application, 4d visualization software, data visualization software, data processing software | Software for 3D/4D image reconstruction. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. | 3d, 4d, image reconstruction, molecular visualization, biocomputing, informatics, rbvi, ucsf, chimera |
is related to: UCSF Chimera is related to: UCSF Chimera has parent organization: University of California at San Francisco; California; USA has plug in: ISOLDE |
NIGMS P41 GM103311 | SCR_015872 | ChimeraX | 2026-08-08 12:00:26 | 2366 | |||||||||
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Short Read Sequence Typing for Bacterial Pathogens Resource Report Resource Website 10+ mentions |
Short Read Sequence Typing for Bacterial Pathogens (RRID:SCR_015870) | SRST2 | sequence analysis software, software resource, software application, source code, data analysis software, data processing software | Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. | genotype analysis, illumina sequence data, mlst database, gene sequence, st, reference gene, short read |
uses: Bowtie uses: SAMTOOLS is listed by: Debian is listed by: OMICtools requires: SciPy requires: Python Programming Language |
infectious disease | NHMRC of Australia 1043830; NHMRC of Australia 1061409; NHMRC of Australia 1061435; Victorian Life Sciences Computation Initiative (VLSCI) VR0082 |
PMID:25422674 | Free, Available for download | OMICS_12777 | http://katholt.github.io/srst2/, https://sources.debian.org/src/srst2/ | http://srst.sourceforge.net/ | SCR_015870 | SRST2: Short Read Sequence Typing for Bacterial Pathogens, Short Read Sequence Typing v2 | 2026-08-08 12:00:43 | 24 | ||
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GrowthToolbox Resource Report Resource Website 1+ mentions |
GrowthToolbox (RRID:SCR_015754) | GFtbox | software resource, software application, simulation software, data analysis software, data processing software | Analysis software for analysis of finite elements and simulations of 3D shape changes in a tissue that result from patterns of growth. It works with Matlab to model biological growth of leaves, petals, and similar organs. | 3d object, finite element, growth, growth pattern, matlab |
uses: MATLAB has parent organization: University of East Anglia; Norwich; United Kingdom |
BBSRC BB/F005997/1; BBSRC BB/F005555/1 |
PMID:21698124 | Free, Available for download | http://cmpdartsvr3.cmp.uea.ac.uk/wiki/BanghamLab/index.php/Main_Page | SCR_015754 | GFtbox | 2026-08-08 12:00:25 | 3 | |||||
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CMake Resource Report Resource Website 10+ mentions |
CMake (RRID:SCR_015875) | authoring tool, software toolkit, software resource, software application, software development tool, software development environment | Software toolkit designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files, and generate native makefiles and workspaces that can be used in the compiler environment of your choice. | software development, compiler, configuration, makefile, workspace | is used by: NiftyPET | PMID:18051095 | Open source, Available for download | SCR_015875 | 2026-08-08 12:00:45 | 25 | |||||||||
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RIPPLELAB Resource Report Resource Website 10+ mentions |
RIPPLELAB (RRID:SCR_015876) | software resource, software application, source code, data visualization software, data processing software | Source code for processing continuous local field potentials (LFP). The interface implements different documented algorithms for HFO detection, and provides several tools for signal visualization and manipulation. | lfp, local field potential, continuous local field potential, computing platform | Free, Available for download | SCR_015876 | RIPPLELAB Multi Analysis EEG Project | 2026-08-08 12:00:26 | 16 | ||||||||||
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CNVcaller Resource Report Resource Website 10+ mentions |
CNVcaller (RRID:SCR_015752) | CNVcaller | sequence analysis software, software resource, software application, source code, data analysis software, data processing software | Software for detecting the integrated copy number variation regions (CNVRs) using population sequencing data. The high-confidence CNVRs are discovered and refined by both individual and population criteria, and the result is a VCF format genotype file which can be used in GWAS/QLT research. | copy number variation, cnv, next-generation sequencing, ngs, population genetic, segmental duplication, absolute copy number | Free, Available for download | SCR_015752 | 2026-08-08 12:00:41 | 40 | ||||||||||
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NiftyPET Resource Report Resource Website 1+ mentions |
NiftyPET (RRID:SCR_015873) | software toolkit, image analysis software, software resource, software application, source code, data visualization software, data processing software | Python software package that offers quantitative PET image reconstruction and analysis with high accuracy and precision. It is written in CUDA C and embedded in Python C extensions. | python, cuda c, python c, pet, image reconstruction, image analysis, bio.tools |
uses: CMake is listed by: Debian is listed by: bio.tools |
DOI:10.1007/s12021-017-9352-y | Free, Available for download, Runs on Windows, Runs on Linux | biotools:niftypet | https://bio.tools/niftypet | SCR_015873 | 2026-08-08 12:00:43 | 7 |
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