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SBML shorthand is a specification and associated Python tooling to interconvert SBML and the shorthand notation. The format was developed by the UK Newcastle systems biology group sometime before 2006. [24] Its aim was to enable modelers to more rapidly create models without having to either write raw XML or use GUI tools.
Interactive Forms is a mechanism to add forms to the PDF file format. PDF currently supports two different methods for integrating data and PDF forms. Both formats today coexist in the PDF specification: [38] [53] [54] [55] AcroForms (also known as Acrobat forms), introduced in the PDF 1.2 format specification and included in all later PDF ...
The Variant Call Format or VCF is a standard text file format used in bioinformatics for storing gene sequence or DNA sequence variations. The format was developed in 2010 for the 1000 Genomes Project and has since been used by other large-scale genotyping and DNA sequencing projects.
The vast majority of modern systems biology modeling software support SBML, which is the de facto standard for exchanging models of biological cellular processes. Some tools also support CellML , a standard used for representing physiological processes.
mzXML is a XML (eXtensible Markup Language) based common file format for proteomics mass spectrometric data. [9] [10] This format was developed at the Seattle Proteome Center/Institute for Systems Biology while the HUPO-PSI was trying to specify the standardized mzData format, and is still in use in the proteomics community.
An open file format is a file format for storing digital data, defined by a published specification usually maintained by a standards organization, and which can be used and implemented by anyone. For example, an open format can be implemented by both proprietary and free and open source software , using the typical software licenses used by each.
The Simplified Molecular Input Line Entry System (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.
The book's format includes opening each chapter with an Issues section that states the underlying questions within the chapter's frameset. Many critical issues are raised throughout each chapter. Some examples of different chapters in the book are HIV and AIDS (16), Drugs and Addiction (14), and The Population Explosion (9). Thought questions ...