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https://github.com/BRAHMS-SystemML/brahms

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.

Proper citation: BRAHMS (RRID:SCR_015642) Copy   

•   Source: SciCrunch Registry

http://phobius.sbc.su.se/

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.

Proper citation: Phobius (RRID:SCR_015643) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/hisat2/index.shtml

Graph-based alignment of next generation sequencing reads to a population of genomes.

Proper citation: HISAT2 (RRID:SCR_015530) Copy   

•   Source: SciCrunch Registry

http://platanus.bio.titech.ac.jp/

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.

Proper citation: Platanus (RRID:SCR_015531) Copy   

•   Source: SciCrunch Registry

https://nxr.northwestern.edu/digital-rat

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.

Proper citation: Elastica2D (RRID:SCR_015858) Copy   

•   Source: SciCrunch Registry

https://www.quantumbiologyinstitute.org/

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.

Proper citation: Quantum Biology Institute (RRID:SCR_015855) Copy   

•   Source: SciCrunch Registry

https://sdrc.stanford.edu/

University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Stanford University.

Proper citation: Stanford Diabetes Research Center (RRID:SCR_015856) Copy   

•   Source: SciCrunch Registry

http://www.ctotstudies.org

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.

Proper citation: Clinical Trials in Organ Transplantation (CTOT) (RRID:SCR_015859) Copy   

•   Source: SciCrunch Registry

http://www.ctotc.org

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.

Proper citation: Clinical Trials in Organ Transplantation in Children (CTOT-C) (RRID:SCR_015860) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/spicodyn/

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.

Proper citation: SpiCoDyn (RRID:SCR_015744) Copy   

•   Source: SciCrunch Registry

http://bioinformaticstools.mayo.edu/research/hybrid-denovo/

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.

Proper citation: Hybrid-denovo (RRID:SCR_015866) Copy   

•   Source: SciCrunch Registry

https://omictools.com/rnacompete-tool

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.

Proper citation: RNAcompete (RRID:SCR_015900) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pdbe/pisa/

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.

Proper citation: PISA (RRID:SCR_015749) Copy   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/chimerax/

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.

Proper citation: UCSF ChimeraX (RRID:SCR_015872) Copy   

•   Source: SciCrunch Registry

https://github.com/katholt/srst2

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.

Proper citation: Short Read Sequence Typing for Bacterial Pathogens (RRID:SCR_015870) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/gftbox/

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.

Proper citation: GrowthToolbox (RRID:SCR_015754) Copy   

•   Source: SciCrunch Registry

https://cmake.org/

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.

Proper citation: CMake (RRID:SCR_015875) Copy   

•   Source: SciCrunch Registry

https://github.com/BSP-Uniandes/RIPPLELAB

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.

Proper citation: RIPPLELAB (RRID:SCR_015876) Copy   

•   Source: SciCrunch Registry

https://github.com/JiangYuLab/CNVcaller

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.

Proper citation: CNVcaller (RRID:SCR_015752) Copy   

•   Source: SciCrunch Registry

https://github.com/pjmark/NiftyPET

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.

Proper citation: NiftyPET (RRID:SCR_015873) Copy   

•   Source: SciCrunch Registry