Search Results for "dna sequence analysis"
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Showing 32 open source projects for "dna sequence analysis"
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Plaso
Super timeline all the things
Plaso (Plaso Langar Að Safna Öllu), or "super timeline all the things," is a Python-based engine designed for automatic creation of timelines in digital forensic investigations. It processes various log files and artifacts to generate a chronological sequence of events, aiding analysts in understanding system activities. -
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gendasm
Generic Code-Seeking Diassembler with Fuzzy-Function Analyzer
...It allows you to enter known starting vectors for a given code image for the micro. It will disassemble the code and follow through branches to assist in the separation of code and data. Its included Fuzzy Function Analyzer companion uses a DNA Sequence Alignment Algorithm to locate similar code in multiple binaries to facilitate reverse-engineering and/or code recovery. The original purpose of the Fuzzy Function Analyzer was to assist in code recovery where the source code for the current binaries got lost, yet the source code for an old binary was retained. The Fuzzy Function Analyzer allows you to match up known functions between the two binaries so you can concentrate on disassembling and reverse engineering the parts that are different and recover the code for the current binary that got lost. -
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quantitative
Quantized transactions python3
...As an open-source educational resource, it’s designed for Python users interested in automatic trading, algorithmic strategies, and financial data analysis. -
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OpenCover
Code coverage tool for .NET 2 and above
OpenCover is a free and open source code coverage tool for .NET 2 and above (Windows OSs only - no MONO), with support for 32 and 64 processes and covers both branch and sequence points. It uses the profiler API that is currently only available to .NET Frameworks running on the Windows platform. OpenCover is an attempt at building a code coverage utility that addresses certain issues in maintaining PartCover support for 64-bit processes. -
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m6811dis
M6811 Code-Seeking Disassembler
The M6811 Code-Seeking Disassembler is a command-line tool that lets you enter known starting vectors for a given code image for the 6811 micro. It will disassemble the code and follow through branches to assist in the separation of code and data. Its companion Fuzzy Function Analyzer uses DNA Sequence Alignment Algorithms to locate similar code in multiple binaries, facilitating reverse-engineering. Originally written to analyze code from GM automotive engine controllers, but is useful anywhere a 6811 micro is being used. Version 1.0 was written in Borland Pascal in April 1996, and updated to v1.2 in June 1999. ... -
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Lexical Analyzer Generator Quex
Generator of lexical analyzers in C and C++. Unicode Supported.
The goal of this project is to provide a generator for lexical analyzers of maximum computational efficiency and maximum range of applications. This includes the support for Unicode (UTF8, UTF16, ...) and a large variety of other encodings directly and via nested converters such as ICU(tm) and IConv. Sophisticated buffer handling allows to operate on plain file streams, on sockets, or manually fed buffer content. 'Ready-to-build' examples explain related concepts and facilitate practical... -
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Prepack
A JavaScript bundle optimizer
A tool for making JavaScript code run faster. Prepack is still in an early development stage and not ready for production use just yet. Please try it out, give feedback, and help fix bugs. Prepack is a tool that optimizes JavaScript source code: Computations that can be done at compile-time instead of run-time get eliminated. Prepack replaces the global code of a JavaScript bundle with equivalent code that is a simple sequence of assignments. This gets rid of most intermediate computations... -
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hopin
list all permutations of a list of given numbers
PermutationCounter (VB.NET with ActiveX) - Lists all permutations of a list of given numbers. -
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OovAide
C++, Java IDE with auto class, sequence, zone, dependency, diagrams
The OovAide project used to be named oovcde. Searching the web will bring up more information about oovcde at this time. The OovAide project is a C++ or Java analysis IDE for Windows or Linux with an automated multi-tasking build system, cross compiler support, an analysis tool based on CLang that creates UML class, component, sequence as well as zone and portion diagrams from C++ or Java source, static analysis and test coverage. The diagrams allow navigation through the source code, and can be edited manually and saved as .SVG files. ... -
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CANStream
An applicaton for CAN bus coms development, testing and validation
CANStream is a .NET application intended to be used for CAN (Controller Area Network) bus communication development, testing and validation. CANStream allows to extensively test any system using CAN communication by sending and receiving CAN frames. Thanks to its powerful built-in mathematical expression evaluator, CANStream can also behave as a real control system feeding back the test device or commanding a third party device with context sensible data. Extended data logging and data... -
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This tool helps you to reverse engineer UML Sequence Diagram for your java program at runtime. It works well with both complex java programs (that have multiple threads) and J2EE applications deployed on Application Servers.
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Tool support for creating FMC* diagrams [Block diagrams, Petri nets, Entity-Relationship diagrams (ERD)] in MS-Visio 2000 and newer. Features: stencils, consistency checking, Petri net simulation, exporter e.g. pdf, ... *Fundamental Modeling Concepts A stripped down version of the stencil set is available for TAM (Technical Architecture Modeling of SAP). This set uses UML notation and contains Block, Activity, Sequence, State, Class, and Component diagrams. It doesn't contain Simulation,...
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Awesome Recurrent Neural Networks
A curated list of resources dedicated to RNN
A curated list of resources dedicated to recurrent neural networks (closely related to deep learning). Provides a wide range of works and resources such as a Recurrent Neural Network Tutorial, a Sequence-to-Sequence Model Tutorial, Tutorials by nlintz, Notebook examples by aymericdamien, Scikit Flow (skflow) - Simplified Scikit-learn like Interface for TensorFlow, Keras (Tensorflow / Theano)-based modular deep learning library similar to Torch, char-rnn-tensorflow by sherjilozair, char-rnn... -
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oovcde
C++ analysis IDE with auto class, sequence, zone, dependency, diagrams
...Downloades from either location work for now. The Oovcde project is a C++ IDE for Windows or Linux with an automated multi-tasking build system, cross compiler support, an analysis tool based on CLang that creates UML class, component, sequence as well as zone and portion diagrams from C++ source, static analysis and test coverage. The diagrams allow navigation through the source code, and can be edited manually and saved as .SVG files. It creates CMake files and can be built using Eclipse or CMake. Export to SQLite is supported. -
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The Panini Language
Better Modularity, Better Concurrency
...The main new feature in Panini is called a capsule. A capsule is like an actor but better because it largely retains the traditional approach for reasoning about programs as a sequence of operations, abstracts away all details of thread creation and locking, and supports fully-automatic compile-time analysis of common concurrency hazards. Panini is simple and efficient. We invite you to try it out. Downloads are available from http://paninij.org/download/ -
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SWAPHI-LS: Alignment on Xeon Phi Cluster
Smith-Waterman long DNA sequence alignment on Xeon Phi clusters
The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host. -
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MSCViewer
A tool for visualization and analysis of logs as sequence diagrams
MSCViewer is a tool intended for debugging of control flows in concurrent, distributed systems. The tool loads logs generated by various entities in the system and visualize a sequence diagram chart for events and interactions. The diagram is fully interactive: entity can be added/removed from the diagram and shuffled; events can be filtered, searched, highlighted and annotated with comments. MSCViewer features integration with a Python interpreter which allows writing Python scripts... -
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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ...
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NGSbinningpytools
Python tools for binning NGS scaffolds to various genomes.
Next generation sequencing has opened new avenues for sequencing prokaryotes which were difficult or either impossible to culture. Now, it is possible to sequence all organisms present in a metagenomic community. However, a critical problem is to determine the host organism for each genomic fragment present in the dataset. This project provides the computational tools for assigning the organismal identity for each genomic scaffold in the given dataset. For more detailed documentation... -
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SPADE
A toolkit for developing and deploying protein structure algorithms.
The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE. -
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PPSeq: Parallel NGS Analysis
Parallel Processing for Next-Generation Sequencing (NGS) Analysis
High-throughput next generation sequencing (NGS) technology has quickly emerged as a powerful tool in many aspects of biomedical research. However, along with its rapid development, the data magnitude and analysis complexity for NGS far exceed the capacity and capability of traditional small-scale computing facilities, such as multithreading algorithms on standalone workstations. To address this issue, here we present a solution using the ever-increasing supply of processing power by massive... -
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Linear Program Solver
Solve linear programming problems
...The main features of LiPS are: ● LiPS is based on the efficient implementation of the modified simplex method that solves large scale problems. ● LiPS provides not just an answer, but a detailed solution process as a sequence of simplex tables, so you can use it for studying/teaching linear programming. ● LiPS gives sensitivity analysis procedures, which allow us to study the behaviour of the model when you change its parameters, including: analysis of changes in the right sides of constraints, analysis of changes in the coefficients of the objective function, analysis of changes in the column/row of the technology matrix. ... -
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DMEAS
DNA Methylation Entropy Analysis Software
DMEAS (DNA Methylation Entropy Analysis Software) is written in C# language. It is a user-friendly DNA methylation analysis tool for DNA methylation pattern visualization and extraction, DNA methylation level calculation and DNA methylation entropy analysis. DMEAS progressively scans the mapping results of bisulfite sequencing reads to extract DNA methylation patterns for contiguous CpG dinucleotides. -
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(Diver is in the process of being moved to GitHub. Please find us at https://github.com/thechiselgroup/Diver. Support requests & messages sent here may never be seen.) Dynamic Interactive Views For Reverse Engineering. Div/er is a set of Eclipse Plugins that aid developers in understanding software. It uses dynamic analysis and reverse engineering to offer views and filters that aid comprehension and discovery.
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GenLab abbreviation of Genetics Laboratory .It is a user-friendly bioinformatics tool to support your bioinformatics lab work. GenLab creates a software user-friendly environment, which makes users to make a large number of protein, DNA, and RNA sequence analysis and excellent graphical viewing. It also provides powerful environment for simulations of Protein 3D molecular models. GenLab typically provides: •User-friendly graphical tools used for finding and working with relevant regions of DNA, RNA, and protein sequences. •Full integration of data input, data management, calculation results. ...
