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Scientific topics: Systems biology 


BcForms tutorial

BcForms is a toolkit for concretely describing the molecular structure (atoms and bonds) of macromolecular complexes, including non-canonical monomeric forms, circular topologies, and crosslinks. BcForms was developed to help describe the semantic meaning of whole-cell computational models...

Scientific topics: Systems biology, Protein modifications, Proteomics

Operations: Validation

Keywords: BiologicalMacromolecules, protein complex, macromolecular complex, crosslink, modification

Resource type: Jupyter notebook

BcForms tutorial https://tess.elixir-europe.org/materials/bcforms-tutorial BcForms is a toolkit for concretely describing the molecular structure (atoms and bonds) of macromolecular complexes, including non-canonical monomeric forms, circular topologies, and crosslinks. BcForms was developed to help describe the semantic meaning of whole-cell computational models . BcForms includes a grammar for describing forms of macromolecular complexes composed of DNA, RNA, protein, and small molecular subunits and crosslinks between the subunits. The DNA, RNA, and protein subunits can be described using BpForms and the small molecule subunits can be described using SMILES. BcForms also includes four software tools for verifying descriptions of complexes and calculating physical properties of complexes such as their molecular structure, formula, molecular weight, and charge: this website, a JSON REST API, a command line interface, and a Python API. This tutorial provides an introduction to BcForms. Systems biology Protein modifications Proteomics BiologicalMacromolecules, protein complex, macromolecular complex, crosslink, modification genomics researchers computational biologists bioinformaticians systems biologists
BpForms tutorial

BpForms is a toolkit for unambiguously describing the molecular structure (atoms and bonds) of DNA, RNA, and proteins, including non-canonical monomeric forms (subunits which compose polymers), crosslinks, nicks, and circular topologies. By concretely describing the molecular structure of...

Scientific topics: Systems biology, Protein modifications, Proteomics, Transcriptomics, Epigenomics

Operations: Validation

Keywords: RNA modification, protein modification, DNA repair, DNA damage, crosslink, nick

Resource type: Jupyter notebook

BpForms tutorial https://tess.elixir-europe.org/materials/bpforms-tutorial BpForms is a toolkit for unambiguously describing the molecular structure (atoms and bonds) of DNA, RNA, and proteins, including non-canonical monomeric forms (subunits which compose polymers), crosslinks, nicks, and circular topologies. By concretely describing the molecular structure of biopolymers, BpForms 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. This tutorial provides an introduction to BpForms. Systems biology Protein modifications Proteomics Transcriptomics Epigenomics RNA modification, protein modification, DNA repair, DNA damage, crosslink, nick genomics researchers computational biologists bioinformaticians systems biologists
Datanator tutorial

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA...

Scientific topics: Omics, Bioinformatics, Systems biology, Cell biology, Molecular biology

Operations: Filtering, Query and retrieval

Keywords: genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis

Resource type: Tutorial

Datanator tutorial https://tess.elixir-europe.org/materials/datanator-tutorial Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. This tutorial provides a brief introduction to the Datanator database and web application. The tutorial illustrates how to search the Datanator database and obtain and refine clouds of data about specific metabolites, RNA, proteins, and reactions of interest. Omics Bioinformatics Systems biology Cell biology Molecular biology genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis mololecular cell biologists systems biologists bioinformaticians Computational biologists modelers
Bioinformática con Ñ

"Bioinformática con Ñ" is a project born in 2013 aimed to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The first release, published in 2014 and edited by Álvaro Sebastián and Alberto Pascual-García, consists on more than 500 pages where the following...

Scientific topics: Systems biology, Bioinformatics

Keywords: introduction to bioinformatics, structural biology, biomolecular databases, Systems biology, phylogenetics, Programming, Sequence Analysis, DNA RNA, Virtual Screening, molecular evolution, molecular dynamics, Molecular docking, normal modes analysis, Proteins, protein folding, protein structure alignment, chromatin structure, intrinsically disordered proteins, data minning, R-programming, parallel computing, bibliography management

Resource type: Book

Bioinformática con Ñ https://tess.elixir-europe.org/materials/bioinformatica-con-n "Bioinformática con Ñ" is a project born in 2013 aimed to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The first release, published in 2014 and edited by Álvaro Sebastián and Alberto Pascual-García, consists on more than 500 pages where the following matters are covered: biomedical databases, sequence analysis, phylogeny and evolution, structural biology, including diverse topics such as docking, virtual screening or molecular dynamics, statistics and R, systems biology, programming skills, data mining, parallel computation, bibliography management and science article writing. Portada: Enrique Sahagún Systems biology Bioinformatics introduction to bioinformatics, structural biology, biomolecular databases, Systems biology, phylogenetics, Programming, Sequence Analysis, DNA RNA, Virtual Screening, molecular evolution, molecular dynamics, Molecular docking, normal modes analysis, Proteins, protein folding, protein structure alignment, chromatin structure, intrinsically disordered proteins, data minning, R-programming, parallel computing, bibliography management Anyone interested in bioinformatics