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http://gmdd.shgmo.org/Computational-Biology/GRS/

A compression tool for efficient storage of Genome Re-Sequencing data. GRS processes genome sequence data without use of reference SNPs and other variants. It can also automatically rebuild the individual genome sequence data using the reference genome sequence.

Proper citation: GRS (RRID:SCR_001008) Copy   

•   Source: SciCrunch Registry

http://ntap.cbi.pku.edu.cn/usage.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl.

Proper citation: NTAP (RRID:SCR_001488) Copy   

•   Source: SciCrunch Registry

https://ptc.bocsci.com/services/ligand-design-for-target-protein.html

Service provider in drug discovery and development. Provides one stop development, which has become strategy in field of small molecular drug discovery. Provides ligand design for target protein to customers to meet new drug discovery goals.

Proper citation: BOC Sciences Ligand Design for Target Protein Service Resource (RRID:SCR_022124) Copy   

•   Source: SciCrunch Registry

https://ptc.bocsci.com/services/target-protein-services.html

Service provider in drug discovery and research. Provides one stop proteolysis targeting molecular drug discovery based on chimeric. Provides target protein services to customers to meet new drug discovery goals.

Proper citation: BOC Sciences Target Protein Services Service Resource (RRID:SCR_022123) Copy   

•   Source: SciCrunch Registry

https://www.pepdd.com/services/hit-identification-in-peptide-drug-discovery.html

Provides Medium or high-throughput screening to perform rapid screening thousands of samples with biological activities at model organism, cell, pathway, or molecular levels, accelerating target analysis procedure; High content screening to analyze the way peptide compound interacts with target at subcellular level; Fragment screening to obtain higher affinity lead ligands by growing low molecular weight chemical fragments into larger drug like molecules;Virtual screening to automatically evaluate large databases with known 3D structures; Artificial Intelligence for difficult targets to support discovering and developing more drug candidates; Knowledge based design in hit identification;Hits identified by NMR screening.

Proper citation: Creative Peptides Hit Identification in Peptide Drug Discovery Service Resource (RRID:SCR_022122) Copy   

•   Source: SciCrunch Registry

https://www.pepdd.com/services/target-analysis-in-silico.html

Services include Binding site identification and druggability assessment, Protein sequence analysis, Protein multiple sequences alignments and selectivity analysis,Analysis of available structural data and protein structure,Homology modeling for targets lacking crystal structures,Design appropriate peptides against specific targets,Water assessment.

Proper citation: Creative Peptides Target Analysis In Silico Service Resource (RRID:SCR_022120) Copy   

•   Source: SciCrunch Registry

https://www.pepdd.com/services/target-validation-in-peptide-drug-discovery.html

Services include Target analysis in silico, Protein sequence analysis and Homology modeling for targets; Target analysis in bioscience, Cell based models.

Proper citation: Creative Peptides Target Validation in Peptide Drug Discovery Service Resource (RRID:SCR_022119) Copy   

•   Source: SciCrunch Registry

https://www.pepdd.com/services/peptide-drug-discovery.html

Services include Structure Based Drug Discovery to design and optimize hits compounds using structural information obtained from X-ray crystallography, cryo-EM or NMR; Cell Based Drug Discovery by selecting correct cell models and culture to study pharmacological and biochemical properties; Ligand Based Drug Discovery.

Proper citation: Creative Peptides Peptide Drug Discovery Service Resource (RRID:SCR_022118) Copy   

•   Source: SciCrunch Registry

https://frostconcepts.org/LeastBridgesGraphs/

Software tool as freely distributed computational method for analyzing distance relationships.

Proper citation: Least Bridges Graphs Mathematica package (RRID:SCR_022115) Copy   

•   Source: SciCrunch Registry

http://www.opensourcebrain.org

A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome.

Proper citation: Open Source Brain (RRID:SCR_001393) Copy   

•   Source: SciCrunch Registry

https://mass-spec.stanford.edu/instruments

System includes Thermo Orbitrap Eclipse Tribid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments.

Proper citation: Thermo Fisher: Orbitrap Eclipse nanoLC/MS system (RRID:SCR_022212) Copy   

•   Source: SciCrunch Registry

https://modelorg-ab.creative-biolabs.com/category-by-species-2.htm

Antibody group provides researchers with functional proteomics research platform. Antibody customization service provider. Custom antibody development team can work with you to create customized antibody solution to meet your specific research needs. Provides monoclonal antibody screening. Prepares monoclonal antibody library to screen monoclonal antibodies for appropriate peptide epitope of each protein.

Proper citation: Creative Biolabs Model Organism Antibodies Service Resource (RRID:SCR_022177) Copy   

•   Source: SciCrunch Registry

https://github.com/ndaniel/fusioncatcher

Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples.

Proper citation: FusionCatcher (RRID:SCR_000060) Copy   

•   Source: SciCrunch Registry

https://github.com/OSS-Lab/ChemChaste

Software tool for simulating spatially inhomogenous biochemical reaction diffusion systems for modelling cell environment feedbacks. Simulation software for spatially organised biochemical systems.

Proper citation: ChemChaste (RRID:SCR_022208) Copy   

•   Source: SciCrunch Registry

https://github.com/rajewsky-lab/spacemake

Software pipeline for processing and analysis of large scale spatial transcriptomics data. Enables reproducible data processing from raw sequencing data to automatically generated downstream analysis reports.

Proper citation: Spacemake (RRID:SCR_022207) Copy   

•   Source: SciCrunch Registry

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

VUIIS (Vanderbilt University Institute of Imaging Science) Image and Data Analysis Core's data processing tools written for MATLAB and, unless stated otherwise, capable of processing 2D/3D images (matrices). These tools are written for ease of use from within MATLAB.

Proper citation: vuTools (RRID:SCR_001704) Copy   

•   Source: SciCrunch Registry

http://dunbrack.fccc.edu/pisces/

Software tool as protein sequence culling server. Used for culling sets of protein sequences from Protein Data Bank (PDB) by sequence identity and structural quality criteria. Can provide lists culled from entire PDB or from lists of PDB entries or chains provided by user.

Proper citation: PISCES (RRID:SCR_022181) Copy   

•   Source: SciCrunch Registry

http://dissect-trans.sourceforge.net/Home

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions.

Proper citation: Dissect (RRID:SCR_000058) Copy   

•   Source: SciCrunch Registry

https://www.olympus-lifescience.com/data/olympusmicro/brochures/pdfs/ix71.pdf?rev=EABE

Research inverted system microscope. Olympus IX2 inverted microscope combined with UIS2 optical system. Used for live cell experiments.

Proper citation: Olympus: IX71 Microscope (RRID:SCR_022185) Copy   

•   Source: SciCrunch Registry

https://github.com/atlab/hdf5matlab

Software library for manipulating neural data files generated in Andreas Tolias Lab.

Proper citation: hdf5matlab (RRID:SCR_003595) Copy   

•   Source: SciCrunch Registry