Search Results for "novel."
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Showing 20 open source projects for "novel."
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Superstaq
Quantum software platform that is optimized across the quantum stack
This repository is the home of the Superstaq development team's open-source work. Our quantum software platform is optimized across the quantum stack and enables users to write quantum programs in Cirq or Qiskit and target a variety of quantum computers and simulators. -
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miRge3
Comprehensive analysis of small RNA sequencing data
An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User Interface (GUI). ... -
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CAMPARI
Software for molecular simulations and trajectory analysis
We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. ... -
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CPAT
RNA coding potential assessment tool
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC , PhyloCSF and RNACode ). ... -
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5
SASA Tool
SWATH-Auto System Analyzer Tool, SASA Tool
SWATH-Auto System Analyzer Tool, SASA Tool, is a novel SWATH platform for non-targeted metabolomics data analysis with an accurate mass spectral library for metabolite identification using SWATH acquisition mode. -
6
miRPV
miRPV: An automated pipeline for miRNA Prediction and Validation in si
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence. System Requirement CPU: AMD64 (64bit) Memory: 2Gb RAM Storage: 5Gb Ubuntu 18.04 -
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FusionCatcher
Somatic fusion-genes finder for RNA-seq data
FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - very good detection of challenging fusion genes, like for example IGH fusions, CIC fusions, DUX4 fusions, CRLF2 fusions, TCF3 fusions, etc... -
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Microarray assosiated motif analyzer
Cis-element prediction tool from microarray data
We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. -
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DACO-algorithm
A novel transcription factor complex prediction algorithm.
...Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. We developed DACO (domain-aware cohesiveness optimization), a novel algorithm that combines protein-protein interaction networks and domain-domain interaction networks with the cluster-quality metric cohesiveness. The metric is locally maximized on the holistic level of protein interactions while sophisticated connectivity constraints on the domain level are utilized to account for the exclusive and thus inherently combinatorial nature of the interactions within such assemblies. ... -
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PPLine
SNP calling, annotation and gene/transcripts expression quantification
PPLine is a Python-based suite aimed to process raw RNA-seq or Exome-seq data. PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration of the results -
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IPS Framework
A simple Python framework for loosely-coupled multiphysics simulations
...However, the design is quite general, and is suitable for many scientific and engineering domains. In addition to plasma physics, it is also being used in the engineering of batteries. One of the novel features of the IPS framework is its ability to support parallelism at multiple levels: components can launch individual parallel tasks, and also launch multiple tasks concurrently. The framework can execute multiple components concurrently, and even multiple simulations, all within the same pool of compute nodes. -
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SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
...Sensitivity is gained by repeatedly running the HMM gene predictor Augustus with varied input parameters, and selectivity by choosing the models with best homology to known proteins and best agreement to the RNA-Seq data. SnowyOwl has successfully predicted genes in 26 novel fungal genomes. The pipeline can be installed locally for high throughput and control over configuration. It can also be run on a remote server through a convenient web interface for occasional use. -
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...Visit http://www.biomedcentral.com/1471-2164/15/858/abstract for the pdf article describing the utility of iMSAT and if you use the program please cite this article as: Andersen and Mills: iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina libraries. BMC Genomics 2014 15:858.
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...Python implementation is more versatile (2D and 3D data). * a Leica file reader, * Steindhard bond orientational order calculation * a VTK file writer 1. Leocmach, M. & Tanaka, H. A novel particle tracking method with individual particle size measurement and its application to ordering in glassy hard sphere colloids. Soft Matter 9, 1447–1457 (2013). https://dx.doi.org/10.1039/C2SM27107A (http://arxiv.org/pdf/1301.7237.pdf)
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Phobos Application
Software for recording rodents' behavior during behavioral tests
...All extracted files can be readily combined to one in order for statistical analyses to be performed. If you use Phobos for your research, please cite: Telonis AG, Margarity M.Phobos: a novel software for recording rodents' behavior during the thigmotaxis and the elevated plus-maze test. Neurosci Lett (2015) doi: 10.1016/j.neulet.2015.05.045 Paper link: http://www.sciencedirect.com/science/article/pii/S0304394015004103 For support, questions or feedback: atelonis@users.sourceforge.net -
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iMir
Integrated pipeline for HT miRNA-Seq data analysis
...The analytical workflow can be challenging for the continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular pipeline, called iMir, integrating multiple open source modules and resource in an automated workflow, devising different statistical approaches to analyze data rigorously. iMir comprises also a Graphical User Interface (GUI), so that the pipeline is particularly suited for biologist and early stage bioinformaticians and produces both graphics and text outputs. -
17
ARDEN
Specificity Control for Read Alignments Using an Artificial Reference
We introduce ARDEN (Artificial Reference Driven Estimation of false positives in NGS data), a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation. -
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FlexGrePPS forms the foundation of a novel antigenic screening methodology that is based on the representation of an entire proteome by near-optimal degenerate peptide pools.
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We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.
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VISPA is a novel development environment for high energy physics analyses, based on a combination of graphical and textual steering. The main goal of VISPA is to support users in prototyping, performing, and verifying a data analysis of any complexity.
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