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'science' section (63/1)


visualisation and analysis for single valued point data

This program provides a graphical interface for the scientific analysis of real valued point data (x,y,z,value). This is primarily targeted towards Atom probe tomography applications, but may prove useful to other applications as well.


sample data for abacas to close gaps in genomic alignments

ABACAS (Algorithm Based Automatic Contiguation of Assembled Sequences) intends to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. . This package contains a test data set as well as sample scripts running some test suite provided by Debian also as autopkgtest.

/main/abacas/abacas

close gaps in genomic alignments from short reads

ABACAS (Algorithm Based Automatic Contiguation of Assembled Sequences) intends to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. . ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs against the reference. The output is then processed to generate a pseudomolecule taking overlapping contigs and gaps in to account. ABACAS generates a comparison file that can be used to visualize ordered and oriented contigs in ACT. Synteny is represented by red bars where colour intensity decreases with lower values of percent identity between comparable blocks. Information on contigs such as the orientation, percent identity, coverage and overlap with other contigs can also be visualized by loading the outputted feature file on ACT.


package for electronic structure calculations (Data files)

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. . ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation). In addition to the main ABINIT code, different utility programs are provided. . This package contains a set of pseudopotentials and example inputs.

/main/abinit/abinit

package for electronic structure calculations

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. . ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation). In addition to the main ABINIT code, different utility programs are provided. . This package contains the executables needed to perform calculations (however, pseudopotentials are not supplied). For a set of pseudopotentials, install the abinit-data package.

/main/abyss/abyss

de novo, parallel, sequence assembler for short reads

ABySS is a de novo, parallel, sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread.


retrieval of DNA or protein sequences

This package collects all those smallish applications that acedb collects under its 'other' target of its Makefile. . efetch: presumably short for 'entry fetch' collects sequence information from common DNA and protein databases.


Advanced Concepts in Electronic Structure III

ACESIII is an electronic structure calculation program with a focus on correlated methods. It is the parallel successor to ACESII, employing the Super Instruction Assembly Language (SIAL) as parallelization framework. . This package contains the documentation, the basis set definitions and the architecture-independent compiled SIAL files.

/main/aces3/aces3

Advanced Concepts in Electronic Structure III

ACESIII is an electronic structure calculation program with a focus on correlated methods. It is the parallel successor to ACESII, employing the Super Instruction Assembly Language (SIAL) as parallelization framework. Features include: . Energies, analytic gradients and analytic hessians for the following methods: * Restricted/unrestricted spin or restricted open-shell Hartree-Fock (HF) * Second-order Moeller-Plesset pertubation theory (MP2) . Energies and analytic gradients for the following methods: * Coupled cluster singles and doubles (CCSD) . Additionally, it can compute energies for the following methods: * Coupled cluster singles and doubles with pertubative triples (CCSD(T)) * Quadratic configuration-interaction singles and doubles (QCISD) . Excited states can be calculated by the following methods: * Qadratic configuration interaction singles and doubles * Coupled cluster equation-of-motion (EOM-CC) . It also includes an internal coordinate geometry optimizer. If analytic gradients are not available, numerical gradients via finite differences are used.


Artificial life and evolution simulator

Achilles is an artificial life and evolution simulator that uses Hebbian neural networks and OpenGL/SDL to simulate life in a simplified environment. It is based on Larry Yaeger's PolyWorld.


rapid adapter trimming, identification, and read merging of gene sequences

This program searches for and removes remnant adapter sequences from High- Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is not available.


rapid adapter trimming, identification, and read merging (example data)

This program searches for and removes remnant adapter sequences from High- Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is not available. . This package provides the example data.


ADIOS Adaptable IO system for simulations - binaries

The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation. By providing an external to the code XML file describing the various elements, their types, and how you wish to process them this run, the routines in the host code (either Fortran or C) can transparently change how they process the data. . This package provides tools for use with ADIOS.


ADIOS Adaptable IO system for simulations - exampes

The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation. By providing an external to the code XML file describing the various elements, their types, and how you wish to process them this run, the routines in the host code (either Fortran or C) can transparently change how they process the data. . This package contains examples for ADIOS.

/main/adms/adms

Automatic device model synthesizer for Verilog-AMS

ADMS is a code generator that converts electrical compact device models specified in high-level description language into ready-to-compile c code for the API of spice simulators. Based on transformations specified in xml language adms transforms Verilog-AMS code into other target languages.


Molecular Simulator

Adun is a biomolecular simulator that also includes data management and analysis capabilities. It was developed at the Computational Biophysics and Biochemistry Laboratory, a part of the Research Unit on Biomedical Informatics of the UPF. . This package contains the AdunCore program and the Adun server. If you want the graphical UI frontend, install the adun.app package.


Molecular Simulator for GNUstep (GUI)

Adun is a biomolecular simulator that also includes data management and analysis capabilities. It was developed at the Computational Biophysics and Biochemistry Laboratory, a part of the Research Unit on Biomedical Informatics of the UPF. . This package contains UL, the Adun GUI frontend.

/main/aegean/aegean

integrated genome analysis toolkit

The AEGeAn Toolkit is designed for the Analysis and Evaluation of Genome Annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.


medical image viewer and DICOM network client

Aeskulap is able to load a series of special images stored in the DICOM format for review. Additionally it is able to query and fetch DICOM images from archive nodes (also called PACS) over the network. Aeskulap tries to achieve a full open source replacement for commercially available DICOM viewers.

/main/aevol/aevol

digital genetics model to run Evolution Experiments in silico

Aevol is a digital genetics model: populations of digital organisms are subjected to a process of selection and variation, which creates a Darwinian dynamics. . By modifying the characteristics of selection (e.g. population size, type of environment, environmental variations) or variation (e.g. mutation rates, chromosomal rearrangement rates, types of rearrangements, horizontal transfer), one can study experimentally the impact of these parameters on the structure of the evolved organisms. In particular, since Aevol integrates a precise and realistic model of the genome, it allows for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences). . The simulation platform comes along with a set of tools for analysing phylogenies and measuring many characteristics of the organisms and populations along evolution.


Sleep-research experiment manager

Aghermann is a program designed around a common workflow in sleep-research, complete with scoring facility; cairo subpixel drawing on screen or to file; conventional PSD and EEG Micrcontinuity profiles; Independent Component Analysis; artifact detection; and Process S simulation following Achermann et al, 1993.

/main/aladin/aladin

Interactive sky atlas for astronomical images and datasets

Aladin is an interactive software sky atlas allowing the user to visualise digitised astronomical images, to superimpose entries from astronomical catalogues or databases, and to interactively access related data and information from the Simbad database, the VizieR service and other archives for all known sources in the field. . Created in 1999 by the Centre de Données astronomiques de Strasbourg (CDS), Aladin has become a widely-used tool of the Virtual Observatory (VO) framework capable of addressing challenges such as locating data of interest, accessing and exploring distributed datasets, and visualising multi-wavelength data. Compliance with existing or emerging VO standards, interconnection with other visualisation or analysis tools, and the ability to easily compare heterogeneous data are the key topics which allow Aladin to be a powerful data exploration and integration tool.

/main/alfa/alfa

Automated Line Fitting Algorithm

ALFA measures fluxes in emission line spectra, such as those of planetary nebulae and HII regions, using a genetic algorithm to rapidly optimise fits to large numbers of lines simultaneously. It can subtract night sky emission lines before fitting the nebular lines if necessary. It can read plain text files containing 1D spectral data, or FITS files containing 1D, 2D or 3D datasets.


program for observing the intermediate steps of algorithm

algotutor is an interactive program for observing the intermediate steps of algorithms ("algorithm animation"). The target audience is computer science students and/or anyone who studies algorithms and/or data structures. One can create data files in plain text format (actually perl anonymous hashes, but one need not care) and let algotutor runs through some predefined algorithm. Then one can step backward and forward through the execution sequence of the algorithm at different levels of details.


Interpolated Variable Order Motifs to identify horizontally acquired DNA

Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into Artemis genome viewer freely available at: http://www.sanger.ac.uk/Software/Artemis/.


NGS copy number algorithms

Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings). . The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg.

/main/altree/altree

program to perform phylogeny-based association and localization analysis

ALTree was designed to perform association detection and localization of susceptibility sites using haplotype phylogenetic trees: first, it allows the detection of an association between a candidate gene and a disease, and second, it enables to make hypothesis about the susceptibility loci.


example files for ALTree

ALTree was designed to perform association detection and localization of susceptibility sites using haplotype phylogenetic trees: first, it allows the detection of an association between a candidate gene and a disease, and second, it enables to make hypothesis about the susceptibility loci. . This package contains the example files for the ALTree package discussed in its PDF manual.


Protein multiple alignment by sequence annealing

AMAP is a command line tool to perform multiple alignment of peptidic sequences. It utilizes posterior decoding, and a sequence-annealing alignment, instead of the traditional progressive alignment method. It is the only alignment program that allows one to control the sensitivity / specificity tradeoff. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation. . The java visualisation tool of AMAP 2.2 is not yet packaged in Debian.


Atomistic Machine-learning Package (python 3)

Amp is an open-source package designed to easily bring machine-learning to atomistic calculations. This project is being developed at Brown University in the School of Engineering, primarily by Andrew Peterson and Alireza Khorshidi, and is released under the GNU General Public License. Amp allows for the modular representation of the potential energy surface, allowing the user to specify or create descriptor and regression methods. . Amp is designed to integrate closely with the Atomic Simulation Environment (ASE). As such, the interface is in pure python, although several compute-heavy parts of the underlying code also have fortran versions to accelerate the calculations. The close integration with ASE means that any calculator that works with ASE ─ including EMT, GPAW, DACAPO, VASP, NWChem, and Gaussian ─ can easily be used as the parent method. . This package provides the python 3 modules.