# Semantic search

- Bmrblib
- Bmrblib is a Python API abstracting the Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) NMR-STAR format (http://www.bmrb.wisc.edu/). 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.

- Brightway2
- Life cycle assessment, Monte Carlo uncertainty analysis, visualization of results

- C-graph
- GNU C-Graph is a tool for visualizing the mathematical operation of convolution underlying natural phenomena susceptible to analysis in terms of engineering signals and systems theory. "C-Graph" is an abbreviation for "Convolution Graph". The package is derived from the BSc. Honours dissertation in Electrical Engineering "Interactive Computer Package Demonstrating: Sampling Convolution and the FFT", Adrienne Gaye Thompson, University of Aberdeen (1983). The package computes the linear convolution of two signals in the time domain then compares their circular convolution by demonstrating the convolution theorem. Each signal is modelled by a register of discrete values simulating samples of a signal, and the discrete Fourier transform (DFT) computed by means of the Fast Fourier Transform (FFT). GNU C-Graph is interactive, prompting the user to enter character or numerical values from the keyboard, dispensing with the learning curve for writing code. The software will be useful to students of signals and systems theory. C-Graph is written in contemporary Fortran. You can find pre-GNU development versions at: <http://codeartnow.com/code/download/c-graph-1/c-graph-version-2-preview>. Adrienne Gaye Thompson is the sole author of GNU C-Graph and looks forward to sharing further development with the Free software community.

- CAGE
- A generic and fairly complete cellular automata simulation engine. CAGE is a fairy generic and complete cellular automaton simulation engine in Python. It supports both 1D and 2D automata, a variety of prepackaged rules, and the concept of "agents" which can move about independently on the map for implementing agent behavior. CAGE comes with numerous examples of fully-functional CA systems, including Conway's Game of Life, Langton's self-reproducing automaton, Langton's "vants," and 1D automata rule explorers. It also comes with simple displayers (including a curses interface for 2D automata). Also included is a unique implementation of a finite state machine (ant.py).

- CCVisu
- The tool CCVisu is a light-weight tool for force-directed graph layout. The tool reads the input graph from a file in RSF (Rigi Standard Format), which is a standard text format for relations. The layout of the graph is computed using standard techniques from force-directed layout. The tool supports several energy models, which can be selected by setting command line parameters. The weighted edge-repulsion LinLog energy model (default) is good for producing layouts that fulfill certain clustering criteria. The Fruchterman Reingold energy model is good for producing layouts that fulfill certain esthetic criteria like uniform edge length. CCVisu stores the resulting layout in certain text file formats such as VRML or SVG, or it displays the layout on the screen.

- CERTI
- CERTI is an HLA RTI. HLA (High-Level Architecture) is a general purpose architecture for distributed computer simulation systems. In HLA systems, the RTI (RunTime Infrastructure) manages data exchange between simulations. CERTI focuses on HLA 1.3 specification and its C++ API (IEEE 1516 will be supported too).

- Ccg
- ccg is a program which enables you to plot ERSL atmospheric gas data from the US National Oceanic and Atmospheric Administration (NOAA) web site.

- Chaco
- Chaco is a software for partitioning graphs mainly intended for parallel computing and scientific simulations. It implements a set of algorithms for this task ranging from a generalization of KL/FM with weighted graphs support to the premiere multilevel algorithms which combine high quality partitioning schemes and low computational costs.

- Cl-ana
- cl-ana is a library of modular utilities for reasonably high performance data analysis & visualization using Common Lisp. (Reasonably means I have to be able to use it for analyzing particle accelerator data). The library is made of various sublibraries and is designed in a very bottom-up way so that if you don't care about some feature you don't have to load it.
The functionality support so far are
- Tabular data analysis: Read-write of large datasets stored in HDF5 files are supported, along with ntuple datasets, CSVs, and in-memory data tables. Users can add their own table types by defining 4 methods and extending the table CLOS type.

- Histograms: Binned data analysis is supported with both contiguous and sparse histogram types; functional interface is provided via map (which allows reduce/fold) and filter.

- Plotting: Uses gnuplot for plotting dataset samples, plain-old lisp functions, histograms, strings-as-formulae, and anything else the user wishes to add via methods on a couple of generics.

- Fitting: Uses GSL for non-linear least squares fitting. Uses plain-old lisp functions as the fit functions and can fit against dataset samples, histograms, and whatever the user adds.

- Generic mathematics: CL doesn't provide extendable math functions, so cl-ana provides these as well as a convenient mechanism (a single function) for using these functions instead of the non-extendable versions. Already included are error propogation and quantities (values with units, e.g. 5 meters) as well as a GNU Octave-style handling of sequences (e.g. (+ (1 2) (3 4)) --> (4 6)).

- CoaSim
- 'CoaSim' is a tool for simulating the coalescent process with recombination and gene conversion under the assumption of exponential population growth. It constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP and micro-satellite haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.

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