Search Results for "rule"

...The Differential Evolution Entirely Parallel method takes into account the individual age, that is defined as the number of iterations the individual survived without changes. The introduced improvements are: (I) allow several oldest individuals to be overwritten by the same number of best ones in the population, (II) new selection rule uses several objective functions in offspring evaluation. RPMs are available at https://build.opensuse.org/project/repositories/home:mackoel:compbio This work is supported by RNF Grant 14-14-00302 and by “5-100-2020” Program of the Russian Ministry of Education and Science. The previous funding included SYSPATHO FP7 project №260429, RFBR grants 10-01-00627-a, 11-01-00573-a, 11-04-001162-a and State Contract with Russian Ministry of Science №14.740.11.0166 and №11.519.11.6041

...We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data. Comparing with the existing software PVAAS, our method has several advantages such as stringent rule-depended filters and statistical filters in each step, detection sequence variants for known splicing events, identification sequence variants in two parts of splicing (junction) separately, detection junction shift events if providing known splicing annotation, evaluating splicing signal, comparing with known DNA mutation and/or RNA editing data, and short running time.

The complexity of cellular networks is an outstanding challenge for documentation, visualisation and mathematical modelling. In this project, we develop a new way to describe these networks that minimises the combinatorial complexity and allows an automatic visualisation and export of mathematical (ODE/rulebased) models.

REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in multiple samples simultaneously and identify differential proportion of RNA editing events in different samples. Moreover, the genome variation can be easily removed by a subprogram fish.pl in our package.

...This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.

Laboratory notebook using version control system and independent date-time stamping (as notarization), in order to ensure record accountability, auditing, and conforming to US FDA 21 CFR 21's rule on electronic records. Please kindly rate this application or drop me an email at [ mauriceling AT acm DOT org ] so that I can hear from you. Otherwise, I have no idea who the users are. Please kindly help.

A rule-based modelling framework for allosteric proteins and biochemical networks.

URBAN – a Unified Rule-Based and Allosteric Network compiler and simulator for quantitative modelling in systems and synthetic biology

This project develops a web-based (JSP) Fuzzy Rule-Based Expert System for analyzing ECG (electro cardio gram) signals & diagnosing Tachi-Arrhythmias. Proj. main blocks: inference engine, knowledgebase, KB editor, explanation, and feature extraction.

dna2abc turns DNA sequences into musical sequences. The key feature is the rule editor; a rule is a regular expression paired with a Tcl script. dna2abc scans a DNA sequence, testing each regular expression: if it matches, the Tcl script is run.

Cellular Automata simulator. Native code (fast) and modular design: update rule, topology, time, measurement, initialization are independant. No GUI (for now...): configuration file (commented default automatically generated) overridable by command line.

UIMA-compliant text analytics using a rule language in which to express context-sensitive constraints on syntactic and semantic text elements.

In silico evolution of biochemical networks using a genetic algorithm combined with a rule-based biochemical network model.