Search Results for "sed"

...It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as SED-ML, SBML and MIRIAM.

The Kinetic Simulation Algorithm Ontology (KiSAO; http://co.mbine.org/standards/kisao) is an ontology of algorithms for simulating and analyzing biological models, as well as the characteristics of these algorithms, their input parameters, and their outputs. In addition, KiSAO captures relationships among algorithms, their parameters, and their outputs. Development of KiSAO has moved to https://github.com/SED-ML/KiSAO/.

This project hosts a library and tools for sharing simulation experiments encoded using SED-ML.

PySCeS CBMPy is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. CBMPy supports the latest standards for encoding CBM models encoding, SBML L3 FBC, COBRA as well as MIRIAM compliant RDF and custom annotations. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently...

A Java library to facilitate SED-ML support for systems biology applications to read, validate, edit, and write SED-ML documents in compliance with MIASE guidelines. Also contains modules to execute simulation tasks and produce outputs. This project also contains the SED-ED editor application for SED-ML.

...The advantages by using CSV as input and output are the following: - Many applications allow an export of its data to CSV or Excel(were it could be saved to CSV) - It is possible to pre- and postprocess the data, e.g removing version numbers before comparing - It is easy to create CSV data from logfiles and other resources by using unix tools like sed or awk - CSV can be loaded into other applications, especially Excel, were it can be formatted by macros for analyzing.

...<word> ::= <alph>+ bnf2xml is a top down recursive parser. Unlike buttom up parsers like gcc(1) or some top downs, bnf2xml is completely unambiguous / resolves ALL conflicts. Slower on ave. for parsing C or than sed(1) for simple searches. Far easier than using flex/C to create a parser. caveate: I do not suggest it's worth while to make a new gcc(1) using bnf2xml. bnf2xml an nth BETA release, but no complains yet.

This project has migrated to GitHub (https://github.com/flintproject/clibsedml).

XPSEDAPI is a cross-platform (programming language agnostic) definition of an application programming interface for working with and manipulating SED-ML documents. Interfaces are defined in Interface Definition Language (IDL) with full documentation.