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http://sourceforge.net/projects/chipmeta/
Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets.
Proper citation: ChIPmeta (RRID:SCR_000054) Copy
https://github.com/SciLifeLab/facs
Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.
Proper citation: FACS (RRID:SCR_000055) Copy
http://sourceforge.net/projects/batman-seq/
A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.
Proper citation: Batman-Seq (RRID:SCR_000048) Copy
Dual channel fluorimeter for fluorescence measurements when calibrated with known concentration to measure compounds at low concentration with low assay volume.
Proper citation: Promega: TBS-380 Fluorimeter (RRID:SCR_018615) Copy
Microplate luminometer that features two optional injectors and reads both glow- and flash-luminescent reactions in 96-well plates. The sensitivity and range enable a wide range of luminescent assays, including Promega bioluminescent reporter, cell-based and biochemical assays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Promega: GloMax 96 Microplate Luminometer (RRID:SCR_018614) Copy
http://www.pirx.com/iMol/index.shtml
Software molecular visualization application for Mac OS X operating system. Tool for chemists and molecular biologists used for handling small and large molecules, loading multiple molecules, moving and rotating them independently, or displaying molecular dynamics trajectory. Allows loading molecules using file formats: PDB, XYZ, MOL2, HIN, CAR, ALC, BIO.
Proper citation: iMol (RRID:SCR_018735) Copy
https://www.biosimulations.org/
Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell.
Proper citation: BioSimulations (RRID:SCR_018733) Copy
https://mass-spec.stanford.edu/instruments
Agilent GC/MS is single quadrupole instrument with electron ionization. GC/MS runs under ChemStation open access software, and trained open access users select from menu of standard methods to analyze their samples.
Proper citation: Agilent: 7890/5975 GC/MS system (RRID:SCR_018695) Copy
Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.
Proper citation: piNET (RRID:SCR_018693) Copy
Sequencing and quantification platform for epigenetics, mutation gene expression analysis, and microbial identification and resistance typing. With its 96-well format, automatic base-calling function, and dedicated software solutions for methylation analysis and assay design.
Proper citation: Qiagen: PyroMark Q96 System (RRID:SCR_018617) Copy
Liquid handling system for production of complex liquid formulations produced from individual stock solutions of various chemical and liquid properties. With a CV of less than 2%.
Proper citation: Rigaku: Alchemist II Liquid Handler (RRID:SCR_018625) Copy
Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites.
Proper citation: rVista (RRID:SCR_018707) Copy
http://funcoup.sbc.su.se/search/
Database of genome wide functional coupling networks. Provides tools to explore predicted networks and to retrieve detailed information about data underlying each prediction. Web service for functional coupling search.
Proper citation: FunCoup (RRID:SCR_018711) Copy
https://github.com/GGFHF/NGScloud2
Software tool for RNA-seq analysis of non model species using cloud computing. Provides user friendly front end to operate Amazon hardware resources and to control workflows of bioinformatic analysis of de novo RNA-seq, reference-based RNA-seq and functional annotation specifically oriented to plant species.
Proper citation: NGScloud2 (RRID:SCR_018716) Copy
http://tools.thermofisher.com/content/sfs/brochures/geneatlas_system_brochure.pdf
System for processing Affymetrix microarrays. Microarray analysis system. Includes array strip and hybridization assembly, Fluidics station, Imaging station.
Proper citation: Thermo Fisher: GeneAtlas System (RRID:SCR_018715) Copy
https://www.thermofisher.com/order/catalog/product/ND-8000-GL
Microvolume UV Vis spectrophotometer for nucleic acid and protein quantification that can measure multiple samples using 1 to 2 uL of samples. Can analyze spectrum of 220nm to 750nm and measure 96 samples in less than six minutes. Can measure multiple samples in one measurement cycle, up to eight samples at one time. Has single sample mode. Can analyze the full spectrum from 220 to 750nm and calculates sample purity ratios 260/280.
Proper citation: Thermo Fisher: NanoDrop 8000 Spectrophotometer (RRID:SCR_018600) Copy
http://www.prisma-statement.org/
Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.
Proper citation: PRISMA (RRID:SCR_018721) Copy
http://www.consort-statement.org/
Standards for transparent trials reporting. Encompasses various initiatives developed by CONSORT Group to alleviate problems arising from inadequate reporting of randomized controlled trials. Main product of CONSORT is CONSORT Statement, which is evidence based, minimum set of recommendations for reporting randomized trials. CONSORT Statement is endorsed by medical journals and leading editorial organizations.
Proper citation: CONSORT (RRID:SCR_018720) Copy
https://cole-trapnell-lab.github.io/monocle3/
Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points.
Proper citation: Monocle3 (RRID:SCR_018685) Copy
https://www.nikonmetrology.com/en-us/product/az100-multizoom
Nikon Instruments AZ100 C1si is macro confocal microscope system combining stereo and compound microscopes into single hybrid imaging system for dynamic imaging of single cells or whole specimens.System covers range of magnifications from 5x to 400x. Has triple nosepiece that can switch magnifications. AZ100 C1si boasts simultaneous 32 channel spectral image acquisition over spectral range of 320 nm in single scan. Simultaneous 32 channel acquisition at 10 nm, 5 nm or 2.5 nm bandwidths, all software controlled, is possible.
Proper citation: Nikon: AZ100 Confocal Microscope (RRID:SCR_018603) Copy
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