Biology Qiuz

Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.

GeneticsLab is an excellent utility for those ones who are learning Biology, Genetics or any related studies. GeneticsLab automates some operations based on the genetic code, so you won't need to do them manually anymore! These are some of the operations

The performance of the level set segmentation is subject to appropriate initialization and optimal configuration of controlling parameters, which require substantial manual intervention. A new fuzzy level set algorithm is proposed in this paper to facilitate medical image segmentation. It is able...


Platforms: Matlab

MGWT: Identification of protein coding regions using the ModifiedGabor-wavelet transform.Sequence of test:F56F11.4.fasta (included into the zip file)http://www.ncbi.nlm.nih.gov/entrez/viewer....de&val=AF099922http://www.vision.ime.usp.br/~jmena/projec...ome_results/F5/References:[1] J. P....


Platforms: Matlab

This program presents the solution to an ode model of the circadian clock, published by Locke et al (2005) 'http://www.nature.com/msb/journal/v1/n1/full/msb4100018.html', in two different ways.A moving plot can show either time series or a limit cycle in 2D or 3D mode, with the user able to...


Platforms: Matlab

Bio link contains solutions to some topics in biology and bioinformatics. The solutions will be made available as soon as they are developed. Therefore they may contain bugs. Please let me know if you encounter a bug so that it can be fixed asap. Most tools will be in JAVA. The jar files can be...


Platforms: Matlab

In biology, graph formalism is prevalently used. This graph package is for you to analysis biomolecular interaction network with the comfort of MATLAB. The package includes algorithm like modularity, clustering coefficient, all-pair shortest path (amazingly fast, great if you have 64-bit) and so...


Platforms: Matlab

This toolbox provides direct access to cancer genomics data from within the MATLAB environment. The toolbox will query the Cancer Genomics Data Server Web API, provided by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center, and return data in a structured format.A tutorial...


Platforms: Matlab

The script is a Matlab implementation of reference gene selection reported inJo Vandesompele et al, "Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes", Genome Biology 2002, 3 (7).


Platforms: Matlab

Dynamic Bayesian networks (DBN) are widely applied in modeling various biological networks, including the gene regulatory network. Due to several NP-hardness results on learning static Bayesian network, most methods for learning DBN are heuristic, that employ either local search such as greedy...


Platforms: Matlab

Estimates the noise standard deviation from an (MRI) image (2D) corrupted with Rician noise based on the skewness of the distribution. This method doesn't depend on the background for noise estimation. Can be used for MR images with and without background.Ref: Jeny Rajan, Dirk Poot, Jaber Juntu...


Platforms: Matlab

PHLAWD (pronounced flawd) allows for the creation of large (mega) phylogenies using NCBI databases. There are binaries available for Linux and MacOSX in the downloads section. PHLAWD takes advantage (or at least part of it) of multi threaded computers and can produce matrices of more than 100,000...


Platforms: Mac

ABNER is a software tool for molecular biology text analysis. It began as a user-friendly interface for a system developed as part of the NLPBA/BioNLP 2004 Shared Task challenge. The details of that system are described in the paper below (Settles, 2004). At ABNER's core is a statistical machine...


Platforms: Mac

Java Fish Hunter is a small game where the player is a sub with a multiple weapons to kill fish. If the fish touch you and you have no shield power, you die. Designed because I wanted to kill the fish from the Marine Biology Case Study.


Platforms: Mac

A cellular automaton is a discrete model studied in computability theory, mathematics, physics, complexity science, theoretical biology and micro-structure modeling. It consists of a regular grid of cells, each in one of a finite number of states, such as "On" and "Off". The grid can be in any...


Platforms: Mac

The Biochemical Abstract Machine (BioCham) is a modelling environment for systems biology, with some unique features for static analysis or for inferring unknown model parameters from temporal logic constraints. BioCham is mainly composed of : a rule-based language for modeling biochemical...


Platforms: Mac

Biomatters was founded on the principle of creating software that can be used by all researchers in their daily work. Our technology converts raw data into meaningful, visual information, simplifying research and ultimately improving efficiency. Biomatters???*a*? flagship software packages are:...


Platforms: *nix

ESBTL (Easy Structural Biology Template Library) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric analysis and advanced constructions.


Platforms: *nix

The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in computational structural biology to facilitate and standardize the development of molecular modeling, design and analysis tools.


Platforms: *nix

ByoDyn (http://cbbl.imim.es/ByoDyn) is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab.


Platforms: *nix