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http://diseasome.eu

A disease / disorder relationships explorer and a sample of a map-oriented scientific work. It uses the Human Disease Network dataset and allows intuitive knowledge discovery by mapping its complexity. The Human Disease Network (official) dataset, a poster of the data and related book (Biology - The digital era, ISBN: 978-2-271-06779-1) are available. This kind of data has a network-like organization, and relations between elements are at least as important as the elements themselves. More data could be integrated to this prototype and could eventually bring closer phenotype and genotype. Results should be visual, but also printable. Creating posters can enhance collaborative work. It facilitates discussion and sharing of ideas about the data. This website initiative is an invitation to think about the benefits of networks exploration but above all it tries to outline future designs of scientific information systems.

Proper citation: Diseasome (RRID:SCR_002792) Copy   

•   Source: SciCrunch Registry

http://www.sbgn.org/Main_Page

The Systems Biology Graphical Notation (SBGN) project aims to develop high quality, standard graphical languages for representing biological processes and interactions. Each SBGN language is based on the consensus of the broad international SBGN community of biologists, curators and software developers. Over the course of its development many individuals, organizations and companies made invaluable contributions to the SBGN through participating in discussions and meetings, providing feedback on the documentation and worked examples, adopting the standard and spreading the word. Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. A list of software packages known to provide (or have started to develop) support for SBGN notations is available.

Proper citation: Systems Biology Graphical Notation (RRID:SCR_004671) Copy   

•   Source: SciCrunch Registry

http://www.proconsortium.org/pro/

An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563).

Proper citation: PR (RRID:SCR_004964) Copy   

•   Source: SciCrunch Registry

http://pdbml.pdb.org/

Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available.

Proper citation: Protein Data Bank Markup Language (RRID:SCR_005085) Copy   

•   Source: SciCrunch Registry

http://www.genmapp.org/

GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options.

Proper citation: Gene Map Annotator and Pathway Profiler (RRID:SCR_005094) Copy   

•   Source: SciCrunch Registry

http://www.zebrafinchatlas.org

Expression atlas of in situ hybridization images from large collection of genes expressed in brain of adult male zebra finches. Goal of ZEBrA project is to develop publicly available on-line digital atlas that documents expression of large collection of genes within brain of adult male zebra finches.

Proper citation: Zebra Finch Expression Brain Atlas (RRID:SCR_012988) Copy   

•   Source: SciCrunch Registry

http://raptorx.uchicago.edu/

Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model.

Proper citation: RaptorX (RRID:SCR_018118) Copy   

•   Source: SciCrunch Registry

http://ultrascan.aucsolutions.com/

Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis.

Proper citation: UltraScan (RRID:SCR_018126) Copy   

•   Source: SciCrunch Registry

https://health.uconn.edu/worm-lab/track-a-worm/

Open source system for quantitative assessment of C. Elegans locomotory and bending behavior. Used for quantitative behavioral analyses to understand circuit and gene bases of behavior. Constantly records and analyzes position and body shape of freely moving worm at high magnification.

Proper citation: Track-A-Worm (RRID:SCR_018299) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/timezone1/

Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes.

Proper citation: TimeZone (RRID:SCR_018564) Copy   

•   Source: SciCrunch Registry

https://github.com/mrc-ide/PhyDyn

Sofware package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. Enables simultaneous estimation of epidemiological parameters and pathogen phylogenies. Epidemiological modelling in BEAST.

Proper citation: PhyDyn (RRID:SCR_018544) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://pinet-server.org

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.bpforms.org

Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts.

Proper citation: BpForms (RRID:SCR_018653) Copy   

•   Source: SciCrunch Registry

https://www.objtables.org

Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.

Proper citation: ObjTables (RRID:SCR_018652) 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://rosie.graylab.jhu.edu/docking2

Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community.

Proper citation: ROSIE (RRID:SCR_018764) Copy   

•   Source: SciCrunch Registry

http://tools.dice-database.org/GOnet/)

Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.

Proper citation: GOnet (RRID:SCR_018977) Copy   

•   Source: SciCrunch Registry

https://delaney.shinyapps.io/CAIRN/

Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions.

Proper citation: CAIRN (RRID:SCR_019101) Copy   

•   Source: SciCrunch Registry