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chemistry (42)

In short, Aletheia is software for getting science published and into the hands of everyone, for free. It's a decentralised and distributed database used as a publishing platform for scientific research. So, Aletheia is software. But software without people is nothing. To comprehensively answer the question what is Aletheia, Aletheia is software surrounded by a community of people who want to change the world through open access to scientific knowledge. For a more in depth explanation, Aletheia is an Ethereum Blockchain application utilising IPFS for decentralised storage that anyone can upload documents to, download documents from, that also handles the academic peer review process. The application runs on individual PCs, all forming part of the IPFS database. This gives us an open source platform that cannot be bought out by the large publishers (and any derivitive works must also be open source) that should also be hard to take down due to the database being spread across the globe in multiple legal jurisdictions. Aletheia is designed to be a resilient platform run transparently by the community, not some black box corporation or editorial board, meaning all users can see the decisions Aletheia is making and have a stake in that decision making process if they so desire. By this nature, Aletheia is decentralised, it has no key person risk. Should the core group who invented Aletheia dissapear Aletheia won't cease to exist, it will continue to be run by the community. The community moderates content through various mechanisms (peer review, reputation scores etc.,) to ensure quality of content.
Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs.
BKchem is a chemical drawing program written in Python. It is platform independent.
Bmrblib is a Python API abstracting the Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) NMR-STAR format ( It allows the writing of NMR-STAR files for BMRB data deposition and the reading and easy extraction of data from files residing in the BMRB data bank, all without knowledge of the Self-Defining Text Archive and Retrieval (STAR) format.
Chemtool is a GTK+-based 2D chemical structure editor for X11. It draws organic molecules easily and store them as a X bitmap file. You can export drawings in XFig format for further annotation, or as Postscript files (using xfig's companion program transfig). The distribution includes a set of sample molecular structure drawings. The package also contains a helper program, cht, to calculate sum formula and (exact) molecular weight from a chemtool drawing file.
DataMelt (DMelt) is an environment for numeric computation, statistical analysis, data mining, and graphical data visualization on the Java platform. This Java multiplatform program is integrated with a number of scripting languages: Jython (Python), Groovy, JRuby, BeanShell. DMelt can be used to plot functions and data in 2D and 3D, perform statistical tests, data mining, numeric computations, function minimization, linear algebra, solving systems of linear and differential equations. Linear, non-linear and symbolic regression are also available. Neural networks and various data-manipulation methods are integrated using powerful Java API. Elements of symbolic computations using Octave/Matlab scripting are supported.
DataWarrior displays multiple graphical views for any tabular data. These views may interactively be updated by applying filters, which dynamically hide rows. Chemical structures and reactions are native data types, such that row filters may be numerical, categorical, textual, or chemical. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns. Chemical descriptors encode various aspects of chemical structures, e.g. the chemical graph, chemical functionality from a synthetic chemist’s point of view, three-dimensional pharmacophore features, or the reaction center of a chemical reaction. These allow for fundamentally different types of molecular similarity measures, which can be applied for many purposes including row filtering and the customization of graphical views. DataWarrior supports the enumeration of combinatorial libraries as the creation of evolutionary libraries. Compounds can be clustered and diverse subsets can be picked. Calculated compound similarities can be used for multidimensional scaling methods, e.g. Kohonen nets. Physicochemical properties can be calculated, structure activity relationship tables can be created and activity cliffs be visualized. Even conformers may be generated and minimized using an built-in MMFF94 forcefield. DataWarrior allows to retrieve all molecules Wikipedia molecules, run structure searches on the ChEMBL database and retrieve three-dimensional structures from the Crystallography Open Database. One may query SQL-databases as well as URLs, which return tabular data. A plug-in interface allows to access further chemical and non-chemical data sources.
E-CELL Simulation Environment
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.
EMAN is a scientific image processing suite designed mainly to perform single-particle reconstructions of individual molecules. In this method, a transmission electron microscope is used to collect images of thousands of individual molecules. A complex series of algorithms then turns the individual 2D images into a high-resolution 3D structure of the molecule. The core of EMAN is a C++ based scientific image processing library.
Fityk is nonlinear curve-fitting and data analysis software. It supports data visualization, separation of overlapping peaks, and least squares fitting using standard Levenberg-Marquardt algorithm, a genetic algorithm, or Nelder-Mead simplex method. It knows common bell-shaped functions (Gaussian, Lorentzian, Pearson 7, Voigt, Pseudo-Voigt) and polynomials, but more sophisticated formulae can be added if needed. It also enables background substracting, data calibration and task automation with a simple script language. It is being developed to analyze powder diffraction patterns, but can be used to fit analytical functions to any kind of data.

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