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Operations: Validation 


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
ObjTables Python tutorials

ObjTables is a toolkit for creating re-usable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances of...

Scientific topics: Data submission, annotation and curation, Data quality management, Data integration and warehousing, Data management

Operations: Validation

Keywords: spreadsheet, schema, table, workbook, worksheet, XLSX, Excel, standard, reuse, compose, integrate, quality control

Resource type: Jupyter notebook

ObjTables Python tutorials https://tess.elixir-europe.org/materials/objtables-python-tutorials ObjTables is a toolkit for creating re-usable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances of classes). ObjTables consists of a format for describing schemas for spreadsheets, numerous data types for science, a markup format for indicating the class and attribute represented by each table and column in a workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. ObjTables is ideal 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. The tutorials provide a brief introduction to the ObjTables format for schemas for spreadsheets, the ObjTables markup syntax for spreadsheets, and the ObjTables Python package for parsing, validating, querying, editing, comparing, merging, splitting, revisioning, migrating, and analyzing spreadsheets. Data submission, annotation and curation Data quality management Data integration and warehousing Data management spreadsheet, schema, table, workbook, worksheet, XLSX, Excel, standard, reuse, compose, integrate, quality control Researchers Scientists Data scientists computational scientists