228 projects tagged "Bioinformatics"

Download Website Updated 05 Jan 2004 Cluster Installation Finishing Scripts

Pop 43.24
Vit 2.36

The Finishing Scripts for Cluster Installations handle specific post-installation configuration that might not be convienent nor possible using existing cluster installation methods. The usual installation process is used to build a reasonably configured node, and the system then reboots into normal mode, achieves network visibility, and executes the finishing script. The finishing script handles all of the finer details of installing packaged or non-packaged software, tweaking installation, setting host/net specific parameters/files, etc. It is controlled via a single, easily modified script.

Download Website Updated 24 Dec 2003 Yawn: Yet Another W* Network

Pop 24.60
Vit 61.71

Yawn (Yet Another {Weird | Wacky | Witty | Wonderful | W*} Network) is a Java framework for training and testing neural networks independently from the neural model and the test environment being used. The models implemented so far are AppART, GasART, fuzzy ARTMAP, and Multi-Layer Perceptron (MLP).

Download No website Updated 22 Dec 2003 Analyze ECGs

Pop 33.54
Vit 1.75

Analyze ECGs is a graphical data analysis tool for use on analog input DAQ data, such as that of RTLab. It is useful for opening the '.nds' file format produced by RTLab's data acquisition program, DAQSystem (it can also open regular ASCII files). Aside from being a general-purpose multichannel analog data editing tool, it also contains custom features useful for analyzing cardiac data. However, it can be used for editing/viewing general-purpose data as well. Additionally, this program can convert '.nds' files to ASCII format data.

Download Website Updated 25 Nov 2003 RTLab

Pop 61.71
Vit 2.08

RTLab is an RTLinux/RTAI-based data acquisition and control application. It is designed to help experimenters design and implement their hard realtime control experiements using higher abstractions than the services offered by RTAI or RTLinux. It is split into two parts. One is a user-space series of C++ classes (written for Qt) which implement a reference application called DAQSystem which is designed to acquire analog input voltage data and display it on the screen. DAQSystem communicates with rtlab.o, the realtime kernel module which is the second part of RTLab. The rtlab.o realtime kernel part is a kernel module that loads into RTLinux or RTAI and is responsible for driving COMEDI hardware for the purposes of data acquisition and realtime control. The module is extensible and features a 'plugin' architecture so that scientists who are savvy C programmers can easily leverage the existing framework for their own custom experiment logic. Experiment logic is specified by writing a kernel modules that gets called back for each scan rtlab.o acquires from the COMEDI hardware. In addition, data visualization and storage facilities exist in user space so that experimenters can instantly see graphical plots of their analog input data as it comes in from the hardware.

Download Website Updated 24 Oct 2003 The VolPack Volume Rendering Library

Pop 41.09
Vit 1.00

VolPack is a portable software library for volume rendering, based on a new family of extremely fast volume rendering algorithms. The library does not use any specialized hardware and is therefore portable to most platforms, yet it achieves very fast rendering times.

Download No website Updated 08 Oct 2003 NeoBio

Pop 12.96
Vit 62.33

NeoBio is a Java class library of computational biology algorithms. The current version consists mainly of pairwise sequence alignment algorithms, such as the classical dynamic programming methods of Needleman and Wunsch (global alignment) and Smith and Waterman (local alignment). A more efficient approach, due to M. Crochemore, G. Landau, and M. Ziv-Ukelson (2002) is also available. All sequence alignment algorithms support simple scoring schemesm as well as substitution matrices such as standard BLOSUM and PAM matrices with constant (linear) gap penalty functions only. Future versions may contain related algorithms such as multiple sequence alignment, database search and protein structure prediction. NeoBio also also provides simple GUI and command line based tools to run the sequence alignment algorithms on DNA and protein sequences.

Download Website Updated 04 Oct 2003 DrawTree

Pop 18.28
Vit 1.73

Drawtree is a program for visualisation of trees. It reads in trees in the Newick format and outputs them in a graphic format. Currently the only supported output format is Encapsulated PostScript, but other formats are planned.

Download No website Updated 23 Sep 2003 MCS PGA 64 Filter Amp Controller

Pop 14.07
Vit 1.02

MCS PGA 64 Filter Amp Controller is a small program that uses Qt 3.x to control the MultiChannelSystems Programmable Gain Amp (http://www.multichannelsystems.com), 64 channel version. This filteramp is a custom piece of equipment typically used in neuronal electronics. This program uses the serial port to set the gains on this programmable amplifier. It is a clone of the Windows version of this program that MCS normally supplies with its filter amp. It is 100% compatible UI-wise with the Windows version.

No download Website Updated 17 Sep 2003 Nomen

Pop 28.07
Vit 1.00

Nomen is a GUI which creates chemical structures from valid IUPAC names. It outputs a 2D view and (optionally) a CML file.

Download Website Updated 15 Sep 2003 Shrubberies - Linux Command Line Viewer

Pop 13.19
Vit 2.39

slcview allows you to fully script creation of clustergrams and tree diagrams from .cdt, .gtr, and .atr files as output by several biologically-oriented clustering programs, namely Cluster and XCluster. Many options allow you control of the output, and, in addition, slcview allows you to create an annotated legend with the same scale of colors as used in your clustergram.


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