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http://oufti.org/

Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions.

Proper citation: Oufti (RRID:SCR_016244) Copy   

•   Source: SciCrunch Registry

https://biochem.missouri.edu/chapman/software.htm

Software for fitting of atomic models into density maps derived from x-ray crystallography or electron microscopy.

Proper citation: RSRef (RRID:SCR_017211) Copy   

•   Source: SciCrunch Registry

https://www.phenix-online.org/documentation/reference/refinement.html

Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB.

Proper citation: Phenix.refine (RRID:SCR_016736) Copy   

•   Source: SciCrunch Registry

http://www.proteometools.org/index.php?id=home

Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research.

Proper citation: ProteomeTools (RRID:SCR_018535) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/mosdepth

Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.

Proper citation: mosdepth (RRID:SCR_018929) Copy   

•   Source: SciCrunch Registry

https://www.glygen.org

Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression.

Proper citation: GlyGen (RRID:SCR_023438) Copy   

•   Source: SciCrunch Registry

https://mibig.secondarymetabolites.org/

MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters.

Proper citation: Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) Copy   

•   Source: SciCrunch Registry

https://hdpm.biomedinfolab.com/netmage/

Web tool for automated generation of interactive disease-disease network visualizations given input PheWAS summary data. Given genetic associations from Phenome-Wide Association Study, disease-disease network can be constructed where nodes represent phenotypes and edges represent shared genetic associations between phenotypes.

Proper citation: NETMAGE (RRID:SCR_021843) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.princeton.edu/conservation/

Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands.

Proper citation: Conservation (RRID:SCR_016064) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/saint-apms/files/

Software tool for upgraded implementation of probabilistic scoring of affinity purification mass spectrometry data. Used for filtering high confidence interaction data from affinity purification mass spectrometry experiments. Used for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

Proper citation: SAINTexpress (RRID:SCR_018562) 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://brainmap.wisc.edu/monkey.html

NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL.

Proper citation: Rhesus Macaque Atlases for Functional and Structural Imaging Studies (RRID:SCR_008650) 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

http://probalign.njit.edu/probalign/login

Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.

Proper citation: eProbalign (RRID:SCR_013247) Copy   

•   Source: SciCrunch Registry

https://masst.gnps2.org/microbemasst/

Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns.

Proper citation: microbeMASST (RRID:SCR_024713) Copy   

•   Source: SciCrunch Registry

http://www.sb.cs.cmu.edu/drem

The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations

Proper citation: Dynamic Regulatory Events Miner (RRID:SCR_003080) Copy   

•   Source: SciCrunch Registry

http://cellprofiler.org

Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types.

Proper citation: CellProfiler Image Analysis Software (RRID:SCR_007358) Copy   

•   Source: SciCrunch Registry

http://ontodog.hegroup.org/index.php

Ontodog is a web-based ontology view generator. It can generate inSubset annotation ontology, user preferred label annotation ontology and subset of source ontology. Simply provide Ontodog input term file (Microsoft Excel file or tab-delimited text file), select one source ontology or enter your own source ontology and SPARQL endpoint, then set the settings for Ontodog output files and get the OWL (RDF/XML) Output files. Ontodog performs the basic ontology modularization-like function, i.e.,it automatically extracts all axioms and related terms associated with user-specified signature term(s). In addition, Ontodog includes extra features: (1) extracting all instance data associated with the retrieved class terms and annotations; and (2) recursively extracting all axioms and related terms indirectly associated with signature terms. More features are being added to Ontodog, such as relabeling preferred names for various ontology terms to fit in with the needs from a specific community. The Ontodog input data requires a source ontology and a list of user-specified signature terms in tab-delimited format. Ontodog provides the template files for generating the signature terms as the input terms file to download. There are several output options that the users can choose based on their needs. With more and more ontologies being developed, Ontodog offers a timely web-based package of solutions for ontology view generation. Ontodog provides an efficient approach to promote ontology sharing and interoperability. It is easy to use and does not require knowledge of SPARQL, script programming, and command line operation. Ontodog is developed to serve the ontology community for ontology reuse. It is freely available under the Apache License 2.0. The source code is made available under Apache License 2.0.

Proper citation: Ontodog: A Web-based Ontology View Generator (RRID:SCR_005061) Copy   

•   Source: SciCrunch Registry

http://www.montana.edu/massspec/index.html

Provides access to mass spectrometers and mass spectrometry expertise. The facility currently maintains the following equipment Waters Synapt-XS Q-IMS-TOF with Waters I-Class UHPLC; Agilent 6538 Q-TOF with Agilent 1290 UHPLC;Agilent 7800 Inductively Coupled Plasma with Laser Ablation (193 nm);Bruker micrOTOF with Agilent 1290 UHPLC; Agilent 6490 Triple Quadrupole Mass Spectrometer; Bruker MALDI Autoflex; Agilent GC-MS; Waters Synapt G2S-i Q-TOF with Ion Mobility.

Proper citation: Montana State University Mass Spectrometry Core Facility (RRID:SCR_012482) 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