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KNIME
KNIME [naim] is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualisation and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network.
Kci
The kc program is a "kinetic compiler". This means it is able to transform chemical equations into simulation programs.
Lamprop
'lamprop' calculates some properties of fiber-reinforced composite laminates. It calculates engineering properties like Ex, Ey, Gxy, thermal properties CTE_x and CTE_y, physical properties like density and laminate thickness, and stiffness and compliance matrices.
Lhendraw
Chemical drawing program for the cdx/cdxml formats. This one tries to be as close and completely as possible to the proprietary reference implementation without forfeiting the KISS principle. It offers a database-less search function and a headless mode for automated editing
Librsb
librsb is a library for sparse matrix computations featuring the Recursive Sparse Blocks (RSB) matrix format. This format allows cache efficient and multi-threaded (that is, shared memory parallel) operations on large sparse matrices. The most common operations necessary to iterative solvers are available, e.g.: matrix-vector multiplication, triangular solution, rows/columns scaling, diagonal extraction / setting, blocks extraction, norm computation, formats conversion. The RSB format is especially well suited for symmetric and transposed multiplication variants. On these variants, librsb has been found to be faster than Intel MKL's implementation for CSR. Most numerical kernels code is auto generated, and the supported numerical types can be chosen by the user at build time. librsb implements the Sparse BLAS standard, as specified in the BLAS Forum documents.
MayaChemTools
MayaChemTools is a growing collection of Perl scripts, modules, and classes to support day-to-day computational discovery needs. The current release of MayaChemtools provides command line scripts for the following tasks:
  • Manipulation of SD, CSV/TSV, Sequence/Alignments, and PDB files
  • Analysis of data in SD, CSV/TSV, and Sequence/Alignments files
  • Information about data in SD, CSV/TSV, Sequence/Alignments, PDB, and fingerprints files
  • Exporting data from Oracle and MySQL tables into text files
  • Properties of periodic table elements, amino acids, and nucleic acids
  • Generation of fingerprints corresponding to atom neighborhoods, atom types, E-state indicies, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs, and topological pharmacophore atom triplets
  • Generation of fingerprints with atom types corresponding to atomic invariants, DREIDING, E-state, functional class, MMFF94, SLogP, SYBYL, TPSA and UFF
  • Calculation of similarity matrices using a variety of similarity and distance coefficients
  • Calculation of physicochemical properties including rotatable bonds, van der Waals molecular volume, hydrogen bond donors and acceptors, logP (SLogP), molar refractivity (SMR), topological polar surface area (TPSA), and so on
Melting Heckert gnu.tiny.png
Melting computes, for a nucleic acid duplex, the enthalpy and entropy of the helix-coil transition, and then its melting temperatures. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA. The program uses the method of nearest-neighbors. The set of thermodynamic parameters can easily be changed, for instance following an experimental breakthrough.
Minfx
The minfx project is a Python package for numerical optimisation, being a large collection of standard minimisation algorithms. This includes the line search methods: steepest descent, back-and-forth coordinate descent, quasi-Newton BFGS, Newton, Newton-CG; the trust-region methods: Cauchy point, dogleg, CG-Steihaug, exact trust region; the conjugate gradient methods: Fletcher-Reeves, Polak-Ribiere, Polak-Ribiere +, Hestenes-Stiefel; the miscellaneous methods: Grid search, Simplex, Levenberg-Marquardt; and the augmented function constraint algorithms: logarithmic barrier and method of multipliers (or augmented Lagrangian method).
OpenBabel
Openbabel is a program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry. The command-line utility that comes with OpenBabel is meant to be a replacement for the original 'babel' program, to translate between various chemical file formats. The library includes the file-translation code as well as utilities to help develop other free software chemistry software.
OpenChrom
OpenChrom is data analysis a tool for gas chromatography and mass spectrometry. Its functionality and algorithms can be extended using a flexible plugin approach. File formats from various vendors are supported.


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