Projects

nemesis

nemesis is an experimental finite element code. nemesis consists of two parts: a C++ core, embedding the Python interpreter, capable of undertaking a wide variety of static/transient/eigenvalue problems accounting for material and/or geometrical nonlinearities, and extras, a set of Python scripts ... [More] that access the core and exploit usability in simple or more complicated tasks, including pre- and post-processing. Some of the available features in nemesis are: ar/beam/triangle/quad/brick elements, uniaxial elastic/hardening/cyclic/viscoplastic materials, von Mises/Mohr-Coulomb multiaxial elasto-viscoplastic materials, initial/modified/full Newton-Raphson and BFGS algorithms, load/displacement/arc-lenght controls and connection to sql databases. [Less]

LaJolla - 3D RNA and protein alignment

LaJolla can perform 3D alignments of RNA and protein structures. It is fast, simple to use and well tested. LaJolla is successfully published in a peer reviewed journal.

structural-testing

Given a subset of the assembler instruction set, write a program and generate the Control Flow Graph for that program. Write a genetic algorithm that using the previously generated graph, finds a set of values for registries EAX, EBX, ECX and EDX that will assure the total coverage of the graph, in ... [More] other words, performing the structural testing of the written program. [Less]

zenpdb

SummaryZenPDB is a Python module to process and analyze macromolecular structures. Macromolecular structures are represented as hierarchically nested python dictionaries, which allows to traverse and manipulate them in a pythonic way and implement structural biology algorithms compactly. This module ... [More] is also useful to establish processing pipelines. ZenPDB is currently capable of parsing and writing PDB files, but PDBML input is also planned. ZenPDB provides fast and versatile Cython implementations of important algorithms in structural biology, namely accessible surface area (ASA) and distance contact calculations by using kd-trees for nearest neighbour look-up. It is crystallography-aware and can construct crystal lattices, unit cells and biological units. DocumentationInstallationDependencies [Less]

lovoalign

lovoalignLovoalign is a new structural alignment package. The methods used for structural alignment are based on Low Order Value Optimization (LOVO) theory. The use of LOVO theory led to the development of fast convergent algorithms that provide very robust optimization of scoring functions. ... [More] Numerical experiments show that the LOVO algorithms implemented here provide the most reliable optimization of the STRUCTAL alignment while being very fast. Simple input parameters can be used to align two structures, a single structure to a whole database, or to perform an all-on-all database structural alignment. See http://www.ime.unicamp.br/~martinez/lovoalign The present site is contains current and previous versions of the package. The alignment can be highly customized, since any subatom selection of the structures, main chains or not, can be aligned by using the "-beta and -ocup" input options. How to install and useCurrently the package is mostly developed for linux/unix users. Under those systems, instalation is done by: 1 - Download the lovoalign.DATE.tar.gz file. 2 - Unpack it and compile it: tar -xzvf lovoalign.DATE.tar.gz cd lovoalign ./configure make(You must have some fortran compiler installed) The directory lovoalign/input contains an example input file for the "lovoalign.sh" script, which is mostly self-explicative, but required the Visual Molecular Dynamics (VMD) package. With this input file, run lovoalign.sh with: lovoalign.sh lovoalign.inp Otherwise, the "lovoalign" executable can be run as a standalone program, as indicated by the instructions in the lovoalign main site. ReferencesPrimary reference, please cite this work when using lovoalign: L. Martinez, R. Andreani, J. M. Martinez. Convergent algorithms for protein structural alignment BMC Bioinformatics, 8:306 2007 Full Text Related work: R. Andreani, J. M. Martinez, L. Martinez, F. Yano. Continuous Optimization Methods for Structural Alignment. Mathematical Pogramming, 112:93-124, 2008 article R. Andreani, J. M. Martinez, L. Martinez Trust region superposition methods for protein alignment IMA Journal on Numerical Analysis, 28, 690-710, 2008. article R. Andreani, J. M. Martinez, L. Martinez, F. Yano. Low Order Value Optimization and Applications. Journal of Global Optimization, 43, 1-22, 2009. article For full text articles go to http://www.ime.unicamp.br/~martinez/lovoalign [Less]

P53 Cancer Rescue Project

P53 Cancer Rescue Project, University of California, Irvine , Samuel A. Danziger, Christopher Wassman, Faezeh Salehi Amiri, Roberta Baronio, Linda Hall, Rainer K. Brachmann, G. Wesley Hatfield, Peter Kaiser, Richard H. Lathrop

iocerco

This library provides a Xquery-Xpath full-text syntax extension for berkeley db xml using xapian db as IR engine. The IR lookup can be made in two different ways: 1) The standard one, that looks for information hidden in non-structured well-specified nodes 2) An approximated way that scans all the ... [More] nodes in the database and provides the user the threshold of proximity to the target node and check for the full-text constraints satisfaction. Next step will introduce a native xml-IR engine (like eXists db) that will allow a modular DB-adaptive structure for our lookups [Less]

patternsbox

This sample eclipse project contains GoF design patterns structural code. To get sources : svn checkout http://patternsbox.googlecode.com/svn/trunk/ patternsbox-read-only

deltaclac

A diffing utility that provides delta calculation services between java objects (java beans to be precise).

Atlas FEA

Open source finite element program. Includes solver and GUI.