## Scientific Computing

- Netlib: a collection of mathematical software, papers, and databases.
- FEniCS Project : a collection of free software with an extensive list of features for automated, efficient solution of differential equations.
- PETSc: a software library for parallel solution of partial differential equations with the MPI standard for all message-passing communication.
- MPI: Message-Passing Interface Standard
- LAM (Local Area Multicomputer): an MPI programming environment and development system for heterogeneous computers on a network.
- MGNet: A repository for information related to multigrid, multilevel, multiscale, aggregation, defect correction, and domain decomposition methods.
- The Finite Element Circus
- Midwest Numerical Analysis Day
- TOP500 Supercomputer Sites

## Optimization

## Computational Molecular Biology

- CHARMM (Chemistry at HARvard Macromolecular Mechanics): A widely-used program package for large scale biomolecular potential energy minimization, molecular dynamics, normal modes and crystal optimizations. It can be used to simulations of proteins, nucleic acids and lipids.
- A short introduction to molecular synamics simulations
- CHARMM tutorial
- DelPhi: Provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution.
- PDB: Protein Data Bank, the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data (about 20,000 structures of proteins and nucleic acids.
- VMD (Visual Molecular Dynamics): A molecular visualization program for displaying, animating, and analyzing biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc.
- 2003 Primer : Genomics and Its Impact on Medicine and Society
- Dictionary of Genetic Terms
- PubMed: a service of the National Library of Medicine, provides access to over 12 million MEDLINE citations back to the mid-1960’s and additional life science journals.
- Annual Conference on Research in Computational Molecular Biology
- ExPASy: SIB Bioinformatics Resource Portal.
- Life Science Directory: This list contains almost exclusively pointers to information sources for life scientists with an interest in biological macromolecules.
- Amino acid structure and properties: from U. Berlin. Includes 3-D interactive models.

## Mathematical Organizations

- AMS: American Mathematical Society
- SIAM
- MAA
- Mathematical Programming Society
- SIAM Activity Group on Optimization
- Society for Mathematical Biology

## Mathematics Archives

- MathSciNet
- Front for the Mathematics ArXiv
- MGNet: a repository for information related to multigrid, multilevel, multiscale, aggregation, defect correction, and domain decomposition methods.
- Mathematics web sites around the world
- Mathematics WWW Virtual Library
- Computational Mathematics Archive
- Internet Mathematics Library

## Tutorials

- FEniCS tutorial (Python)
- The Python Tutorial; Python
- is a programming language that lets you work more quickly and integrate your systems more effectively.

- The Python Language Reference
- The Python Standard Library
- Python Scripting for Computational Science
- A Practical Introduction to Matlab
- Maple Essentials
- Programming in C: A Tutorial
- C++ Language Tutorial
- Writing HTML