Search Results for "packages"

SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients.

...The purpose of a statistical analysis is to establish our level of trust in both the data and in the conclusions we draw from that data. Both the GrowthRate and CGR2 packages are

> CStone wiki: https://sourceforge.net/p/cstone/wiki/Home/ Related Software: 1. CStone: (See wiki) 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/

DBSolveOptimum is a stand-alone software tool for the construction and analysis of mathematical models of biological systems. It is a succession and extension of DBSolve 5 and DBSolve 7, which were popular tools for systems biology. In addition to the capabilities of these software packages, DBSolveOptimum is implemented with new tools for extended data analysis and multiple simulations, which are important for simulation of virtual clinical trials and application of modern modeling techniques, like quantitative systems pharmacology, to problems arising in drug research and development. By this time, DBSolveOptimum has been successfully tested and applied for the development and analysis of both systems pharmacology and conventional PK/PD models of drugs. ...

BioNLP-Corpora is a repository of biomedically and linguistically annotated corpora and biomedical data sources. There are many resources available in separate packages in this project.

This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.

...Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits. Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. Citation: Chikkagoudar, S., Wang, K., & Li, M. (2011). ...

A number of software packages are available to generate DNA MSAs evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages).

...RNA seq programs included are TopHat, CuffLinks, CuffDiff, CuffMerge, FastQC, and trimming using the FastX toolkit. DressUp facilitates RNA seq programs by streamlining various packages into a single script. That script executes the RNA seq programs on a batch cluster system. Upon execution of the script, jobs are submitted to the cluster depending on attributes set up in the configuration file. Program options can be modified in the main script "DressUp", and PBS options can be modified from the HeaderFiles directory.

RMol is an R script with a collection of functions to link information of SD/Molfile structure databases with powerful graph analysis packages in R.

The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html

BIL++ is a set of standalone C++ packages for data processing in Bioinformatics (Graph mining, Bayesian networks, Genetic algorithm, Discretization, Gene expression data analysis, Hypothesis testing).

J2dPathway project are composed of several packages: J2dPathway(biological pathway viewer), Pyrus Pathway Editor (biological CAD), and DNASequenceViewer (platform-independent sequence viewer).

We use R (www.r-project.org) in order to generate a greater specificity and sensitivity of protein identification by Mass Spectrometry. These functions are implemented as add-on packages to the open source GPL software R.

Set of Java packages to apply Genetic Algorithms to any kind of problem. Various genetic operators are implemented and an example shows of how the system could be applied to digital circuit evolution.

fsap is a bundle of R packages that implements several models and processes used in Fisheries Science. The main purpose is to allow a Fisheries Scientist or Student to do a full stock assessment within the R environment.