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https://systemsbiology.columbia.edu/genome-center

Core sells sequencing data and bioinformatic analytics services to the scientific community. Core aims to permit the development of research on sequencing protocols and encourage collaboration with clinicians to develop the next generation genomic DNA testing.

Proper citation: JP Sulzberger Columbia Genome Center (RRID:SCR_012650) Copy   

•   Source: SciCrunch Registry

http://www.msg.chem.iastate.edu/gamess/

Software program for ab initio molecular quantum chemistry. GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Capabilities include using nuclear gradients for automatic geometry optimization, modeling of solvent effects, computation of the energy hessian for prediction of vibrational frequencies, as well as computation of nuclear wavefunctions. The program can also compute variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities.

Proper citation: Gamess (RRID:SCR_014896) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_GenomicsDNAAnalysis.aspx

Core facility that provides sequencing services, access to equipment and consultation on experimental design and data analysis. Available instruments include the Life Technologies Ion Torrent PGM and Ion Proton sequencers. Core also provides amplification-free analysis of RNA expression using the NanoString nCounter, and additionally provides sequencing and analysis services to investigators outside of SBP. Included in the cost of sequencing is basic bioinformatic analysis (SNP/InDel calling, transcript abundance). Lastly, the core also provides advice on experimental design, and guidance on the capabilities of next-generation sequencing.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Genomics DNA Analysis Facility (RRID:SCR_014866) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_HighContentScreening.aspx

Core facility that provides access to the HTS plate and liquid handling infrastructure of the screening center, as well as the screening center�s cell culture facility. Other services include assay development, screening, and data analysis/mining expertise and services for high content screens. Consultation from the team is available for high content image-based screens including sample preparation, image acquisition, image analysis, image data management, and algorithm development.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute High-content Screening Core Facility (RRID:SCR_014869) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_Cheminformatics.aspx

Core facility that supports assay development, high throughput (HTS), ultra-high throughput (uHTS), and high-content screening (HCS) activities performed at the Conrad Prebys Center for Chemical Genomics by providing databases and tools for compound registration and inventory, HTS plate formatting and tracking, HTS and HCS bioassay data processing as well as related data and information handling. Data mining and reporting are also facilitated with a user-friendly database interface. The Cheminformatics core also supports the design and obtaining of appropriate compound collections, as well as SAR follow-up of hits, hit-to-lead optimization and in silico screening through docking and other molecular modeling approaches.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Cheminformatics Core (RRID:SCR_014875) Copy   

•   Source: SciCrunch Registry

http://www.scripps.edu/florida/technologies/cbs/index.html

Core facility that provides access to genome-wide collections of cDNAs and siRNAs that can be used to interrogate cellular models of signal transduction pathways and phenotypes. Services include cell lines, hit-picking clones and various screening sets, and access to equipment.Provides instruments:Analyst Molecular Devices,Embla Molecular Devices, Envision Perkin Elmer, Platemate Matrix, Tecan M200, Wellmate Matrix.

Proper citation: Scripps Research Institute Florida Cell Based High Throughput Screening Core Facility (RRID:SCR_014877) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_NMR.aspx

Facility that acts as a centralized shared resource for NMR studies on proteins, peptides, small molecules, and carbohydrates in solution or in solid state. It provides instrumentation and expertise for NMR data collection. It also provides consultation with investigators on the feasibility of NMR for structural studies of protein candidates, as well as the optimal method to obtain solution structures and binding information by multi-dimensional NMR techniques. It can also train users in basic spectrometer operations, trouble-shoot for instrumental and operational problems, and set up NMR experiments for users as requested.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute NMR Facility (RRID:SCR_014861) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_ProteinAnalysis.aspx

Facility that provides a variety of analytical services focused on biophysical characterization of structural and functional properties of proteins in solution, under native, non-denaturing conditions. Examples of services include quality control of protein samples (folding, stability, aggregation); measuring molecular weight of proteins, protein complexes, oligomers and assemblies; charcaterizing protein conformation and shape in solution; determining oligomeric state of protein (including stoichiometry and Kd for self-association) and measuring protein binding to proteins, peptides, small molecules, compounds, metals, nucleotides and other ligands (including determination of equilibrium (Kd) and kinetic rate (kon, koff) constants, stoichiometry, binding enthalpy and entropy).

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Protein Analysis Core (RRID:SCR_014862) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/integrative-genomics-and-bioinformatics-core/

Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications.

Proper citation: Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) Copy   

•   Source: SciCrunch Registry

http://chicagodiabetesresearch.org/cores/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 30,2023. Core facility that provides analytic support for a wide range of projects in diabetes translation research ranging from program evaluation to cost-effectiveness analysis.

Proper citation: Chicago Center for Diabetes Translation Research Quantitative Analysis Core (RRID:SCR_015208) Copy   

•   Source: SciCrunch Registry

http://mbcf.dfci.harvard.edu

Core offers services for genomic next-generation sequencing library preparation, sequencing and analysis applications including RNAseq, ChIPseq, ATACseq, CRISPR screening, whole genome methylation profiling, targeted resequencing, single-cell RNAseq, exome sequencing, and more. Performs bioinformatics analysis such as integration of multi-omics datasets or specialized analyses. Genomics core technology platforms include Illumina NovaSeq6000, NextSeq500s, MiSeqs, MiniSeq. High throughput sample preparation is performed on Beckman Coulter Biomek FX and i7 systems. Low throughput samples are prepared by technical staff.

Proper citation: Dana-Farber Cancer Institute Molecular Biology Core Facility (RRID:SCR_009754) Copy   

•   Source: SciCrunch Registry

http://montana.eagle-i.net/i/0000012b-00be-4e65-df3b-3fdc80000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research.

Proper citation: Montana State University Bioinformatics Core Facility (RRID:SCR_009937) Copy   

•   Source: SciCrunch Registry

http://structuralbiology.cau.edu.cn/PlantGSEA/

Websever for gene set enrichment analysis of plants. Used for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets.

Proper citation: PlantGSEA (RRID:SCR_016866) Copy   

•   Source: SciCrunch Registry

http://www.mqtldb.org/

Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES).

Proper citation: mqtldb (RRID:SCR_018002) Copy   

•   Source: SciCrunch Registry

https://atlas.kpmp.org/

Atlas is set of interactive tools built to promote retrieval, exploration, discovery, and analysis of Kidney Precision Medicine Project data by greater research community. Datasets available in repository are combination of raw and processed data from KPMP participant biopsies and reference tissue samples.

Proper citation: Kidney Tissue Atlas (RRID:SCR_021626) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/products/clc-main-workbench/

A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.

Proper citation: CLC Main Workbench (RRID:SCR_000354) Copy   

•   Source: SciCrunch Registry

http://www.biochem.mpg.de/en/rd/baumeister/research/ContentCEM/Software_development

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software platform for low dose electron tomography (ET) for all processing steps: acquisition, alignment, reconstruction, and analysis. Requires: Matlab R2008a and Image Processing Toolbox (V6.1)

Proper citation: Acquisition and Analysis for Electron Tomography (RRID:SCR_000192) Copy   

•   Source: SciCrunch Registry

http://bmsr.usc.edu/software/targetgene/

MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7

Proper citation: TARGETgene (RRID:SCR_001392) Copy   

•   Source: SciCrunch Registry

http://www.preger.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods.

Proper citation: Primate Embryo Gene Expression Resource (RRID:SCR_002765) Copy   

•   Source: SciCrunch Registry

http://www.fmri.wfubmc.edu/cms/software

Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.

Proper citation: Advanced Neuroscience Imaging Research Laboratory Software Packages (RRID:SCR_002926) Copy   

•   Source: SciCrunch Registry