Tools   Select Another Resource Report Type

http://amp.pharm.mssm.edu/CREEDS/

Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures.

Proper citation: CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) Copy   

•   Source: SciCrunch Registry

http://neuroexpresso.org/

Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression.

Proper citation: NeuroExpresso (RRID:SCR_015724) Copy   

•   Source: SciCrunch Registry

https://www.rosettacommons.org/home

Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

Proper citation: Rosetta (RRID:SCR_015701) Copy   

•   Source: SciCrunch Registry

https://github.com/sorgerlab/ashlar

Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration.

Proper citation: ASHLAR (RRID:SCR_016266) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/fermi-lite

Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling.

Proper citation: fermi-lite (RRID:SCR_016112) Copy   

•   Source: SciCrunch Registry

http://acb.qfab.org/acb/glam2/

Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets.

Proper citation: Glam2 (RRID:SCR_016129) Copy   

•   Source: SciCrunch Registry

http://zhanglab.ccmb.med.umich.edu/EDTSurf/

Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening.

Proper citation: Edtsurf (RRID:SCR_016083) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/Harmonizome/

Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources.

Proper citation: Harmonizome (RRID:SCR_016176) Copy   

•   Source: SciCrunch Registry

http://sonorus.princeton.edu/hefalmp/

HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool.

Proper citation: Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/allopathfinder

Software application and code base that allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space. The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins. It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or "walking" of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. They are investigating which residues are likely to participate in allosteric communication pathways. The application is a collection of C++/QT code, suitable for reproducing the computational results of the paper. (PMID 17900617) In addition, they provide input and alignment information to reproduce Figure 3 (a key figure) in the paper. Examples provided will show users how to use AlloPathFinder with other protein families, assumed to exhibit an allosteric communication. To run the application a multiple sequence alignment of representative proteins from the protein family is required along with at least one protein structure.

Proper citation: Allopathfinder (RRID:SCR_002702) Copy   

•   Source: SciCrunch Registry

http://pilgrm.princeton.edu

PILGRM (the platform for interactive learning by genomics results mining) puts advanced supervised analysis techniques applied to enormous gene expression compendia into the hands of bench biologists. This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner. This capability allows domain experts to quickly and easily generate hypotheses about biological processes, tissues or diseases of interest. Specifically PILGRM helps biologists generate these hypotheses by analyzing the expression levels of known relevant genes in large compendia of microarray data. PILGRM is for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). PILGRM produces publication quality PDFs usable as supplementary material to describe the computational approach, standards and datasets. Each PILGRM analysis starts with an important biological question (e.g. What genes are relevant for breast cancer but not mammary tissue in general?). For PILGRM to discover relevant genes, it needs examples of both genes that you would (positive) and would not (negative) find interesting. Lists of these genes are what we call standards and in PILGRM you can build your own standards or you can use standards from common sources that we pre-load for your convenience. PILGRM lets you build your own literature-documented standards so that processes, disease, and tissues that are not well covered in databases of tissue expression, disease, or function can still be used for an analysis.

Proper citation: PILGRM (RRID:SCR_004749) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/lapdftext/

Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise.

Proper citation: lapdftext (RRID:SCR_006167) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi?process=home

A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.

Proper citation: ESEfinder 3.0 (RRID:SCR_007088) Copy   

•   Source: SciCrunch Registry

https://www.brown.edu/research/facilities/transgenic-and-gene-targeting/home

MTGTF is to support the investigators in using genetically modified mouse models in Brown University, affiliated hospitals and academic institutions in Rhode Island and other states. Provides services of molecular design and generation of transgenic and knock-out mouse models as well as general advice on use and management of such models. Conventional ES cell gene-targeting system is employed to serve as alternative or to fill the limitations of CRISPR/Cas9 system. Routine services include genotype analysis, sperm or embryo cryopreservation and storage, rederivation, in vitro fertilization (IVF). Other services, such as mouse vasectomy, embryo transfer, colony scale-up, intracytoplasmic sperm injection (ICSI) are also available. New services requiring MTGTF resources can be created through request.

Proper citation: Brown University Transgenic and Gene Targeting Core Facility (RRID:SCR_017690) Copy   

•   Source: SciCrunch Registry

https://flowcore.hsc.wvu.edu/

Facility provides instrumentation and scientific support for single cell analysis and sorting. Routinely performs analysis of both eukaryotic and prokaryotic cells for expression of intracellular and extracellular proteins, cell cycle, cell proliferation, cytokine production, and cell sorting based on expression of cell surface antigen(s) and/or expression of genetically engineered intercellular fluorescent proteins.

Proper citation: West Virginia University Flow Cytometry and Single Cell Core Facility (RRID:SCR_017738) Copy   

•   Source: SciCrunch Registry

https://mbim.uams.edu/research-cores/flow-cytometry-core-facility/

Core provides flow cytometry instrumentation and analysis. Instruments include Fortessa, FacsAria and Image Stream.

Proper citation: Arkansas University College of Medicine Flow Cytometry Core Facility (RRID:SCR_017741) Copy   

•   Source: SciCrunch Registry

https://www.usd.edu/medicine/basic-biomedical-sciences/proteomics-core

Core provides proteomics services to researchers from South Dakota and the surrounding region to rapidly analyze and identify protein expression patterns in their experimental systems.Develops experimental design, protocols, data analysis and interpretation.Provides consulting and advice in grant proposal, as well as data preparation to be submitted to proteomics journal according to requirements.Offers training in use of common equipment such as scanner, spot cutter, imaging software, technique and protocol issues, and sample preparation.

Proper citation: South Dakota University SD BRIN Proteomics Core Facility (RRID:SCR_017743) Copy   

•   Source: SciCrunch Registry

http://hts.ku.edu/

Core offers high throughput screening of large chemical libraries of compounds to identify novel chemical entities that target biological system of interest.Provides target identification and validation, assay development, high throughput screening, hit confirmation, data mining and medicinal chemistry to facilitate hit to lead development.

Proper citation: Kansas University at Lawrence High Throughput Screening Laboratory Core Facility (RRID:SCR_017752) Copy   

•   Source: SciCrunch Registry

https://my.ilabsolutions.com/service_center/show_external/4003

Core specializes in cell, protein, and small molecules analysis as well as cell culture techniques. Services include:2-D gel electrophoresis, 2-D DIGE, LC-MS/MS, HPLC, flow cytometry, fluorescence-activated cell sorting (FACS), cell and tissue culture, and immortalization of cell lines. Our staff works closely with investigators to help design, perform, and analyze experiments.Offers training and assistance in flow cytometry, tissue culture, and operation many of our walk-up instruments.Instruments:Cell Sorter: FACS Aria III, BD Biosciences;Flow Cytometers, analyzers:C6, Accuri/BD Biosciences;Novocyte 3000, ACEA Biosciences;software for analysis: FSC Express, DeNovo software;LC-MS/MS: 6460 Triple Quadrupole, Agilent;Typhoon Trio Scanner, GE Lifesciences;Blood Analyzer: Hemavet 950, Drew Scientific.Plate Readers:;Victor Nivo 5F, Perkin Elmer;Luminometer: Centro XS, Berthold.Services:Cell Sorting (FACS);2-D gel electrophoresis/2D-DIGE;LC-MS/MS analysis of compounds; Cell immortilization.

Proper citation: Nemours/A.I.duPont Hospital for Children Cell Science Core Facility (RRID:SCR_017854) Copy   

•   Source: SciCrunch Registry

https://www.unmc.edu/vcr/cores/vcr-cores/animal-behavior/index.html

Provides investigators with expertise, equipment, and space that is required to conduct innovative acoustic, behavioral, and cognitive research with focus on rigor, reproducibility, and maintaining the highest standards of animal welfare.

Proper citation: University of Nebraska Medical Center Animal Behavior Core Facility (RRID:SCR_018830) Copy   

•   Source: SciCrunch Registry