Search Results for "assembly source code" - Page 5
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Showing 246 open source projects for "assembly source code"
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...In addition to accurate quantitation, iMet-Q provides the charge states and isotope ratios of detected compounds. It accepts input data in netCDF, mzXML, and mzML format and exports quantitation results in csv and txt format. The software source code is freely available under the license of GPL2.
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Madeline 2.0 Pedigree Drawing Engine
Madeline 2.0 Pedigree Drawing Engine (PDE)
The Madeline 2.0 Pedigree Drawing Engine is a pedigree drawing program designed to handle large and complex pedigrees with an emphasis on readability and aesthetics. PLEASE NOTE THAT as of 2015.09.30, the most current Madeline source code tree is now maintained on GITHUB at https://github.com/piratical/Madeline_2.0_PDE . -
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SPA
SPA: a short peptide assembler for metagenomic data
...Craig Venter Institute, San Diego, CA {yyang,czhong,syooseph}@jcvi.org * Corresponding author SPA is available in binary on 64 bit Linux OS. SFA-SPA is available in binary and source for 64 bit Linux OS. -
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rainbow
short reads clustering and local assembly
Efficient tool for clustering and assembling short reads, especially for RAD. -
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Insulin IP Calc
Insulin infusion protocol calculator
...The infusion protocol calculator is based on the updated "Yale Insulin Infusion Protocol" http://bit.ly/1DaVfUd and American Association of Clinical Endocrinologists (AACE) blood sugar targets. http://inpatient.aace.com/ . Source code requires Xamarin Studio & Android SDK to compile. -
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parSRA
Portable Framework for the Parallel Execution of Short Read Aligners
...It uses the following techniques in order to improve scalability: 1) a fast splitting of the input reads using the FUSE kernel module available in most of current Linux distributions; 2) a balanced on-demand distribution of the reads based on the shared locks of UPC++, an extension of C++ for parallel computing that follows the Partitioned Global Address Space (PGAS) paradigm. parSRA is portable as its configuration file allows the users to parallelize the execution of existing SRA tools without the need to modify the source code of parSRA or the aligner. -
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Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface.
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Virus QSP Modeling
C++ and Python code for simulating RNA virus replication
Stochastic simulation model of poliovirus Sabin-to-Mahoney genetic state transition (C++ code). Models genotypes, virus populations, and quasispecies cloud. Simulates replication error and copy-choice recombination. Various parameters guiding the model are user-specified. Python code post-processes simulation output to produce report files. -
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RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.
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DEAPathways
Differential Expression Analysis for Pathways
This project contains the source code associated with the PLoS Computational Biology publication: "Differential Expression Analysis for Pathways". The paper text can be found here: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002967 -
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CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
...IPDPS 2011: 1199-1211 [3] Edans Sandes, Alba Melo. CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences. PPOPP 2010: 137-146 The latest source code can be found in Github. See the MASA project at https://github.com/edanssandes/MASA-CUDAlign -
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Shoal
A lot of fish in a shoal, in a gigantic scientific ocean.
Ours organization website GCModeller.org is coming online soon! Shoal Shell is the sub project for the "genome-in-code"(http://code.google.com/p/genome-in-code/) virtual cell modelling project of the bacteria Xcc 8004. Shoal Shell aim at provide the modelling tool and the debugging tool for the GCModeller virtual cell modelling, And from the extendible library package, shoal shell can manage to accomplish the entire modelling job for any other bacteria species. Shoal Shell Project... -
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A basic and easy java program to make black and white identikit drawing ,with a library of face elements that you can also modify and expand without limit !Source code available. Also available a very rough base for a 3D construction of the face.
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AMOS
AMOS is a collection of tools for genome assembly
AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation. -
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Automatic cell lineage reconstruction
Automatic segmentation and tracking for 3D time-lapse microscopy
...Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities." *Please cite this paper if you use this code for your research -
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The target system of this project is to develop mathematically efficient program code generator from cellml like biological models described by mathematical markup languages.
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MICA-aligner
Next-generation sequencing short reads aligner based on Intel® MIC
Latest Code in GitHub: https://github.com/aquaskyline/MICA-aligner To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC’s limitation and the extra parallelism inside each MIC core. Experiments on aligning 150bp paired-end reads show that MICA using one MIC board is ~4.85 times faster than the CPU-(multi-core)-based BWA-MEM and about the same speed as the GPU-based SOAP3-dp. Furthermore, MICA’s... -
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SOAP3-DP
Fast, Accurate and Sensitive GPU-based Short Read Aligner
Latest Code on GitHub: https://github.com/aquaskyline/SOAP3-dp SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina... -
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mitoMaker
mitoMaker - a mitochondria assembly and annotation script
mitoMaker is a pipeline script developed to simplify the assembly and automatic annotation of mitochondrial genomes, based on raw NGS reads and an optional target reference. mitoMaker calls well known assemblers and algorithms, such as SOAPdenovo, MIRA and blast+ and parses their results providing easily readable outputs, such as FASTA, GENBANK, SEQUIN, PNG and others. General pipeline: 1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches... -
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Pathosphere
Code supporting Pathosphere.org
Pathosphere.org is a website designed to: Provide a means for rapid pathogen detection and characterization, and establish a more collaborative model for software development and sharing. Create an analytical environment that will enable the use of collaborators' software from anywhere, but ensure the security of analytical capabilities and data. Establish a common web front end that will capture a dynamic and changing set of analytical features. Allow users to work with the... -
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MSL
http://dx.doi.org/10.1002/jcc.22968
...Reference: Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A. Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). J Comput Chem. 2012 vol. 33 pages 1645-61 Download article at http://dx.doi.org/10.1002/jcc.22968 -
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reynard
A novel universal genome assembly tool
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mullpy
Multilabel-learning library built on python
Mullpy is a machine-learning library that mainly aim to solve multi-label problems. It is classifier independent, has many ensemble capabilities (diversity methods like bagging, random subspaces, etc.) and automated results presentation (Excel, images as ROC or class-separated info, etc.). It is fully configurable. At the moment supports Neural Networks and classifiers defined in files. It is working on python3.3. -
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...This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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mitoMaker
mitoMaker - a mitochondria pipeline wrapper script
Mitomaker is a pipeline wrapper, result analyzer and automated annotator, written in Python v2.7, that, with the help of other programs, builds, analyzes, looks for the best build and annotates target genomes (such as mitochondria and cloroplast). It could be used with other targets, such as specific genes, or transcriptomes, even though that is not it's primary goal, nor thoroughly tested. After various attempts to build different mitochondrial genomes in the lab I studied, a general...
