149 projects tagged "Medical Science"

Download Website Updated 02 Mar 2001 PDBCat

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Pop 18.71
Vit 1.00

PDBCat can be used to manipulate and process PDB files using commonly available text-processing tools such as Perl, awk, etc. The Brookhaven Protein Data Bank stores atomic coordinate information for protein structures in a column-based format which is designed to be read easily read by FORTRAN programs. PDBCat converts the ATOM and HETATM records of PDB files from this column-based format to a field-based one that is more easily processed by standard Unix tools.

Download Website Updated 02 Mar 2001 Mol_Volume

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Pop 16.25
Vit 1.00

Mol_Volume calculates the volume of a macromolecule by a method somewhat akin to the Monte Carlo method, namely, by measuring how many vertices of a dense regular grid happen to be within the probe radius of the molecule's atoms. The volume is then calculated as V = V_grid * N_near / N_total = N_near * V_per_node.

Download Website Updated 02 Mar 2001 Mindy

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Pop 17.20
Vit 1.00

Mindy is a very simple serial molecular dynamics program derived from NAMD source code. It currently uses xplor parameter and structure files. The program is written in very straightforward C++.

Download Website Updated 02 Mar 2001 MatDCD

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Pop 16.73
Vit 1.00

MatDCD is a Matlab package for reading/writing DCD-formatted molecular dynamics trajectory files. It supports Charmm and xplor-format DCD files, it can read both big- and little-endian storage formats, and it can specify which atom indices to load without having to load the entire file.

Download Website Updated 02 Mar 2001 FlipDCD

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Pop 16.06
Vit 1.00

FlipDCD is a small utility for reversing the endianism of binary DCD trajectory files from Charmm and NAMD. This can be useful when running simulations on one architecture and visualizing or analyzing the results on another. FixDCD is a tiny utility to modify the header of an X-PLOR DCD file to make it readable by programs expecting Charmm DCD files, at the expense of a Timestep size value in the header.

No download Website Updated 16 Mar 2006 CatDCD

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Pop 21.54
Vit 1.80

CatDCD functions much like the Unix "cat" command: it concatenates DCD files into a single DCD file. You can also use CatDCD to write only selected atoms to the final DCD file.

Download Website Updated 26 Oct 2011 E-Cell System

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Pop 130.10
Vit 12.43

E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components, driven by multiple algorithms with different timescales, to coexist. The core library is written in C++ with a Python binding, and frontend software uses Python.

Download Website Updated 27 Oct 2013 Mumps Compiler

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Pop 133.31
Vit 20.95

Mumps Compiler is a compiler for a subset of the Mumps language, a language used mainly in healthcare. It is compatible with most operating systems with a standard C compiler.

Download No website Updated 12 Oct 2013 Open Infrastructure for Outcomes

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Pop 82.52
Vit 3.20

OIO is a Web-based metadata/data management front-end which is built using Zope and works with Postgresql. No programming is required to build and manage Web-forms or to perform data mining/analysis on the collected data. It is in production at the Harbor/UCLA Medical Center for clinical outcomes management and research data. Forms created with OIO and hosted on any OIO server can be downloaded as XML files. Once downloaded from the "Forms library" and imported into an OIO server, the necessary database tables are automatically recreated and the imported forms become immediately available to the users of that OIO server.

Download Website Updated 29 Dec 2001 The VP7 WKP

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Pop 21.98
Vit 3.19

The VP7 Way Kool Project is a GTK application which simulates a laboratory experiment with radioactive nuclei. The user can choose between many predefined radioactive sources or create new ones. The number of decayed nuclei and the activity of the source can be determined with a built-in counter. The beam can be attenuated with shields of paper, aluminium, and/or lead.

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Project Spotlight

The Sound of Sorting

A demo program containing many integer sorting algorithms.

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Project Spotlight

edtFTPj/PRO

A Java library supporting FTPS (FTP over SSL) and SFTP.