Qualitative dynamics semantics for SBGN process description
نویسندگان
چکیده
منابع مشابه
Systems biology An algorithm for automated layout of process description maps drawn in SBGN
Motivation: Evolving technology has increased the focus on genomics. The combination of today’s advanced techniques with decades of molecular biology research has yielded huge amounts of pathway data. A standard, named the Systems Biology Graphical Notation (SBGN), was recently introduced to allow scientists to represent biological pathways in an unambiguous, easyto-understand and efficient man...
متن کاملAn algorithm for automated layout of process description maps drawn in SBGN
MOTIVATION Evolving technology has increased the focus on genomics. The combination of today's advanced techniques with decades of molecular biology research has yielded huge amounts of pathway data. A standard, named the Systems Biology Graphical Notation (SBGN), was recently introduced to allow scientists to represent biological pathways in an unambiguous, easy-to-understand and efficient man...
متن کاملSBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps
BACKGROUND Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats such as BioPAX and SBGN. Effective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need ...
متن کاملSemantics of the Process Description Language
The Process Description Language (PDL) [2] was developed as a Java extension for description of processes. It describes process as a set of activities that are partially ordered (in time) using a mechanism based on high level Petri Nets especially ICNets[1]. The aim of this paper is to give precise and formal definition of the PDL language semantics. For this purpose the theory of Abstract Stat...
متن کاملSoftware support for SBGN maps: SBGN-ML and LibSBGN
MOTIVATION LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The librar...
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ژورنال
عنوان ژورنال: BMC Systems Biology
سال: 2016
ISSN: 1752-0509
DOI: 10.1186/s12918-016-0285-0