Search Results for "two"

*NOTICE* The official software(NGSpop) will be updated soon, so please visit us in 2/29. Thank you.

This project, initially developed at University College London, contains programs to perform rigid, affine and non-linear registration of nifti or analyse images. Two versions of the algorithms are included, a CPU- and a GPU- (using CUDA) based implementation.

lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/

BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.

...Information regarding the project and funding can be found at http://ricediversity.org, and within the corresponding publications and how-to videos: How to videos: http://vimeo.com/cornellricelab PANorama1.0 (Crowell et al. 2014): http://www.plantphysiol.org/content/165/2/479.short PANorama2.0 (Crowell et al. 2016): (http://goo.gl/vQux5Z)

...We demonstrate its (1) generality, by reconstructing cell lineages in four-dimensional, terabyte-sized image data of fruit-fly, zebrafish and mouse embryos, acquired with three different types of fluorescence microscopes, (2) scalability, by analyzing advanced stages of development with up to 20,000 cells per time point, at 26,000 cells min-1 on a single computer workstation, and (3) ease of use, by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities." ...

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 reads with different lengths. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. Citation: Luo R, Wong T, Zhu J, Liu C-M, Zhu X, et al. (2013) SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner. ...

The target system of this project is to develop mathematically efficient program code generator from cellml like biological models described by mathematical markup languages.

Open Source project for the development of the IEEE 11073-20601 reference implementation.

This is a project for Andre to share CellML related tools he works on that other people might find useful.

An algorithm to compute molecular graph descriptors considering the stereochemistry of the molecular structure, based on our previously introduced signature molecular descriptor. The algorithm can generate two types of descriptors, one which is compliant with the Cahn-Ingold-Prelog priority rules, and a faster one based on our previous definition of a directed acyclic graph that isaugmented to a chiral molecular graph.

OpenCV powered image stack analyser for data extraction and preparation. Can be used in conjunction with nanocalcFX. You can get sample data at the NISA homepage. Currently in pre-alpha state.

FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.

Foad is an open source software which receive an EKG Signal from scanner, WFDB database or heart sensors. Finding patient disease started by taking Fourier transform (FFT) from input signal and extract a single cycle. Based on some heuristic algorithm the most important feature like P , Q , R , S , T captured and feed to trained neural network. and so the final decision made by CNN library. As mentioned before this software also capable do some image processing on scanned paper to lower...

Juggernaut is a high throughput out of core sequence assembly algorithm. This program is very useful in assembly projects involving massive number of short reads which originate from high coverage of the genome.

Opensource software projects for genetics and genomics from Sage Bionetworks.

FRASS is developed for RNA Structure Comparison. It allows one to compare the 3D structures of two RNA molecules and to scan a database containing all the known RNA 3D structures against a single query.

vcif is an open source software for validation of Crystallographic Information Files. It supports lexical, parser and dictionary validation (DDL 1 and 2 are fully supported, DDLm draft partially supported)

Palex is a two-stage biological sequence searching system. Library will contain functions for searching patterns, palindromes and structures in DNA sequence.

Code for predicting the 2-dimensional folding with minimum energy of a given RNA sequence. The code was written and originally released by Rune Lyngso.

The program predicts the optimal folding of all consecutive substrings of length L of an RNA sequence of length N in O(NL) time. The algorithm is based on two papers: Wexler, Zilberstein, Ziv-Ukelson (2007), and Horesh, Wexler, Ziv-Ukelson ,Unger (2008)

Disloki is a modified version of Loki (loki.homeunix.net) which works as a Boinc application. The project also contains support programs to create and maintain a Loki based boinc project.

Biological Annotation Tool is a general-purpose high speed environment for manipulating biological sequence annotations in multiple input and output formats. A plugin-style API permits much extensibility.

EGEETomo aims at creating a grid oriented tool to perform tomographic reconstruction on the field of electron microscopy. It is specially designed to work on the EGEE grid but could be easily adapted to other grid platforms.

We use R (www.r-project.org) in order to generate a greater specificity and sensitivity of protein identification by Mass Spectrometry. These functions are implemented as add-on packages to the open source GPL software R.