Search Results for "software solution design"

PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. ...

Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR (qPCR, rt-PCR, etc.), and Sanger sequencing. Gemi can parse large dataset of sequences efficiently. Python source code is available upon request. Milestone:...

Traditional methods for isolation of microsatellites (SSRs) are often expensive and time consuming. Nowadays is easier and cheaper to obtain genomic data from next generation sequencing. Then, at least two software need to be applied in order to obtain SSR primers of SSR flanking sequences for PCR assays. Here we propose new software that allows the user to work with several sequences for PCR primer design in one step.

...Philosophy The main goal is to create a set of tools that enable the computational study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a distance or edit a dihedral) to complex applications (protein modeling or design). MSL is developed in the Senes Lab at the University of Wisconsin-Madison and by a team of developers/users from other research laboratories. Reference: Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A. Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). ...

The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.

These classes are useful for signal processing in Matlab or C++. They bring together tools and methods which may be used interchangeably for Matlab and C++. Their initial use is in conjunction with work towards my degree at UC Berkeley.

This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. "Novel computational methods for increasing PCR primer design effectiveness in directed sequencing". BMC Bioinformatics 2008, 9:191.

ORFer reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. ORFprimer is an extended software package for high throughput PCR primer design for biological sequences

The BioArray Software Environment (BASE) v1.2 is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. PrognoChip-BASE extends BASE v1.2.16, providing more functionalities.

This software collection is for a DNA sequencing laboratory. It is used to design closure/finishing reactions following a shotgun sequencing experiment. It requires a draft assembly composed of contigs and scaffolds.

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 structural biology to facilitate the development of molecular modeling, design and analysis tools.

Multilayered feed-forward neural network software written in C++. Backpropagation and RPROP are available as training algorithms. Design goals: speed of execution when calculating the output to new data, and quality of training (preprocessing: PCA).

IslandEv distributes a Genetic Algorithm (like <a href="/projects/jaga">JaGa</a>) across a network (see <a href="/projects/distrit">DistrIT</a>) using an island based coevolutionary model in which neighbouring islands swap migrating individuals every

The platestats software aims to provide a convenient solution for analyzing the results of biological assays performed in 96- and 384-well plates.

Before year 2045, we want to create a "software development lab" that will allow to write "from scratch" the DNA of a creature, the "content" of it's first cell, and the components of the solution in which it will grow, to simulate it's life.