an automated particle selection system for electron microscopy. The application was written by James Chen in Niko Grigorieff laboratory at Brandeis.

a program suite that contains tools and examples for extracting data from many structure determination applications and assembles the data into mmCIF format for wwPDB deposition.

(Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches.

The CRISPRCasFinder program enables the easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program with improved specificity and indication on the CRISPR orientation. MacSyFinder is used to identify cas genes, the CRISPR-Cas type and subtype.

TomoEED is an optimized software tool for fast feature-preserving noise filtering of large three-dimensional (3D) tomographic volumes on CPUs and GPUs. The tool is based on the anisotropic nonlinear diffusion method. It has been developed with special emphasis in the reduction of the computational demands by using different strategies, from the algorithmic to the high performance computing perspectives. TomoEED manages to filter large volumes in a matter of minutes in standard computers.

Python modules and command-line utilities for electron microscopy of biological samples.

an HDF5 read plugin for XDS. NEGGIA presents HDF5 data to XDS in a fully parallelized way, directly and without interconversion and speeds up the processing of HDF5 data.