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http://www.cbs.dtu.dk/services/DiscoTope/

Web server to predict discontinuous B cell epitopes from protein three dimensional structures.

Proper citation: DiscoTope (RRID:SCR_018530) Copy   

•   Source: SciCrunch Registry

https://www.ddg-pharmfac.net/AllerTOP/

Web server for in silico prediction of allergens. Alignment free server for in silico prediction of allergens based on main physicochemical properties of proteins. Used to predict the route of allergen exposure: food, inhalant or toxin.

Proper citation: AllerTop (RRID:SCR_018496) Copy   

•   Source: SciCrunch Registry

https://www.epimodel.org/

Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics.

Proper citation: EpiModel (RRID:SCR_018539) Copy   

•   Source: SciCrunch Registry

https://github.com/blackrim/phyutility

Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI.

Proper citation: Phyutility (RRID:SCR_018545) Copy   

•   Source: SciCrunch Registry

https://github.com/lmb-embrapa/machado

Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code.

Proper citation: Machado (RRID:SCR_018428) Copy   

•   Source: SciCrunch Registry

http://diana.imis.athena-innovation.gr/DianaTools

Collection of tools to provide algorithms, databases and software for interpreting and archiving data in systematic framework ranging from analysis of expression regulation from deep sequencing data, annotation of miRNA regulatory elements and targets to interpretation of role of ncRNAs in various diseases and pathways. Includes target prediction algorithms microT v4 and microT-CDS, databases of experimentally verified miRNA targets on coding and non-coding RNAs like TarBase v7.0 and LncBase, and software capable of identifying potentially altered molecular pathways by expression of single or multiple miRNAs , mirPath. Provides Web Server (v5.0) to support series of workflows enabling users to perform miRNA analyses.

Proper citation: DIANA Tools (RRID:SCR_018425) Copy   

•   Source: SciCrunch Registry

https://www.flidea.tech/flic-support

R Code used to analyze FLIC data. Functions are provided to examine interactions with food for single well and food choice experiments when fly makes physical contact with liquid food.

Proper citation: R scripts for FLIC data analysis (RRID:SCR_018386) Copy   

•   Source: SciCrunch Registry

https://prosa.services.came.sbg.ac.at/prosa.php

Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling.

Proper citation: ProSA-web (RRID:SCR_018540) Copy   

•   Source: SciCrunch Registry

https://mygene.info/

Web service for querying or retrieving gene annotation data.

Proper citation: MyGene.info (RRID:SCR_018660) Copy   

•   Source: SciCrunch Registry

https://github.com/quest-bih/barzooka

Software automated screening tool that detects bar graphs of continuous data in preprints submitted to bioRxiv. Used for detection of bar graphs for continuous data in BioRxiv preprints.

Proper citation: Barzooka (RRID:SCR_018508) Copy   

•   Source: SciCrunch Registry

https://github.com/OHDSI/CohortMethod

Software R package for performing new user cohort studies in observational database in OMOP Common Data Model.

Proper citation: CohortMethod (RRID:SCR_018511) Copy   

•   Source: SciCrunch Registry

http://cucurbitgenomics.org/

Database to facilitate genomic and genetic data distribution, analysis, mining and integration for cucurbits. To store, mine, analyze, integrate and disseminate Cucurbitaceae family datasets and to provide central portal for cucurbit research and breeding community. Central portal for comparative and functional genomics of cucurbit crops.

Proper citation: CuGenDB (RRID:SCR_018401) Copy   

•   Source: SciCrunch Registry

https://www.planmeca.com/software/

Software tool as 3D imaging software. Flexible and intuitive all-in-one dental software platform. Provides set of tools to meet imaging needs by any dental facility.

Proper citation: Planmeca Romexis (RRID:SCR_018403) Copy   

•   Source: SciCrunch Registry

http://biorender.com

Web tool for graphical illustrations for biological systems by BioRender. Used for articles and presentations. Collection of pre made icons and templates from life science fields for scientific illustrations. Customized icons possible on request.

Proper citation: Biorender (RRID:SCR_018361) Copy   

•   Source: SciCrunch Registry

http://silico.biotoul.fr/pge/

Web tool implementing positional gene enrichment analysis of gene sets for high resolution identification of over represented chromosomal regions.

Proper citation: Positional Gene Enrichment (RRID:SCR_018360) Copy   

•   Source: SciCrunch Registry

https://sedfitsedphat.nibib.nih.gov/software/default.aspx

Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.

Proper citation: SEDFIT (RRID:SCR_018365) Copy   

•   Source: SciCrunch Registry

https://github.com/grecolab/TinderMIX

Software tool as framework for dose and time dependent gene expression analysis which aims to identify groups of genes that show dynamic dose response behaviour. Software R package to cluster gene expression by contour plots. Used to analyse toxicogenomics data with multiple dose levels and time points and to identify expression patterns with respect to both variables and to cluster molecular features.

Proper citation: TinderMIX (RRID:SCR_018364) Copy   

•   Source: SciCrunch Registry

http://gpcr.biocomp.unibo.it/predgpi/pred.htm

Prediction system for GPI-anchored proteins. Used to predict presence of GPI-anchor and position of omega site. Prediction server based on support vector machine for discrimination of anchoring signal, and on Hidden Markov Model for prediction of most probable omega site. Method for screening whole proteomes.

Proper citation: PredGPI (RRID:SCR_018363) Copy   

•   Source: SciCrunch Registry

http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi

Web server for anisotropy of diffraction limit and Bayesian estimation of structure amplitudes by Global Phasing Limited. Server uses DEBYE and STARANISO software to perform anisotropic cut off of merged intensity data, to perform Bayesian estimation of structure amplitudes and to apply anisotropic correction to data.

Proper citation: STARANISO (RRID:SCR_018362) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

Web tool for conserved domains searching within protein or coding nucleotide sequence.

Proper citation: Conserved Domains Search (RRID:SCR_018729) Copy   

•   Source: SciCrunch Registry