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Showing 29 open source projects for "problem a"
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This software solves the Phylogeny problem using Median Networks. Exact and heuristic methods available. Input: an alignment and a reversible stepmatrix, output: (sub)optimal trees and their combinations. Steiner problem solver included.
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QSdpR
Viral Quasispecies Reconstruction software based on QSdpR algorithm
This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population. -
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MPprimer
a program for reliable multiplex PCR primer design
Background: Multiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template using more than one primer set (comprising a forward primer and a reverse primer) in one tube, has been widely used in clinical and environmental microbiology studies. However, primer design for multiplex PCR is still a challenging problem and several factors need to be considered. These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer dimerization, and the inability to separate and purify DNA amplicons of similar electrophoretic mobility. Results: A new program named MPprimer was developed to help users design primer sets for multiplex PCR with high reliability. ... -
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MaxInfo
Transcriptome assembler for RNA-seq
...Assembling transcripts from reads are challenging because of the unpredictable uncertainties arising from completing full genome structure with very partial observations. MaxInfo tackles this problem by explicitly reducing the inherent uncertainties in the biological system caused by missing information. -
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Lab Inventory
Rediscover the Simplicity www.atgclabs.com
...Lab Inventory can provide you with the advanced functionality you require enabling you to regain control of your stuff. If you are experiencing problems using the Lab Inventory System then please report your problem to support@atgclabs.com If you want to get priority help, need to get up to speed quickly, require some training or need full production support, request customization to your unique work flows or new features, please contact sales@atgclabs.com Join us on www.linkedin.com/groups/Lab-Inventory -
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MuffinEC
Multi-technology, INDEL aware error correction for NGS data
...We are developing the 2nd version of MuffinEC. The beta version is already available online. The changes are listed in the VERSION_HISTORY file. Please report any problem you may encounter at the email address specified in the README file. We really appreciate your help. -
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owl reasoning over big biomedical data
A OWL reasoning framework for the analysis of big biomedical data
...OWL reasoning method is ideally suitable for problems involved complex semantic associations because it is able to infer logical consequences based on a set of asserted rules or axioms. MapReduce framework isused to solve the problem of scalability. In our experiment, we focus on the discovery of associations between Traditional Chinese Medicine (TCM) and Western Medicine (WM). -
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Animal Studies
Animal Studies
...Animal Studies application is web-based and completely customizable, with Animal Studies it is very simple to create, change and distribute data flows using an iterative approach. Animal Studies puts all the information right at your fingertips. If you are experiencing problems using the Animal Studies System then please report your problem to support@atgclabs.com -
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ExSTraCS
Extended Supervised Tracking and Classifying System
...Michigan-style LCS algorithms constitute a unique class of algorithms that distribute learned patterns over a collaborative population of of individually interpretable IF:THEN rules, allowing them to flexibly and effectively describe complex and diverse problem spaces. ExSTraCS was primarily developed to address problems in epidemiological data mining to identify complex patterns relating predictive attributes in noisy datasets to disease phenotypes of interest. ExSTraCS combines a number of recent advancements into a single algorithmic platform. It can flexibly handle (1) discrete or continuous attributes, (2) missing data, (3) balanced or imbalanced datasets, and (4) binary or many classes. ... -
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Lab Processes
Rediscover the Simplicity http://www.atgclabs.com/
...The Lab Processes application is web-based and completely customizable, with Animal Studies it is very simple to create, change and distribute data flows using an iterative approach. Animal Studies puts all the information right at your fingertips. If you are experiencing problems using Lab Processes then please report your problem to support@atgclabs.com -
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RT-alignment
Graph-based time alignment algorithms for multiple LC-MS datasets
...The main challenge in this task lies in correcting retention time shifts, which are inevitable even on the same instrument and under the same elution conditions. For large-scale studies, multiple instruments or multi-week experiments are often required, which exacerbates the problem. We present a new graph-based time alignment algorithm that can align these less similar LC-MS maps, which cannot be effectively handled by existing methods. -
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Visual Blast
GUI to accelerate protein and nucleotide BLAST analysis
BLAST (Basic Local Alignment Search Tool) is a popular program that retrieves a library of sequences that resemble the query. The major problem experienced by new users of BLAST revolves around constructing syntactically and semantically correct command line, getting input files into acceptable formats and assessing the output. Visual BLAST is a Graphical User Interface written in C# and it was developed to simplify the parameters setting for BLAST searches. Visual BLAST aims to make BLAST searches accessible to a wider audience with no bioinformatics skill and to facilitate usage among the existing. ... -
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adLIMS
adLIMS: a Laboratory Information Management System with ADempiere
Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the genome of target cells. ... -
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cmotif
A method for mining conditional phosphorylation motifs
...The discovery of phosphorylation motifs is a very valuable work in bioinformatics. Although several algorithms have been proposed to uncover phosphorylation motifs, the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. In this paper, we propose an algorithm called C-Motif for a non-redundant identification of significant phosphorylation motifs. In tests with real data including both non-kinase-specific and kinase-specific phosphorylation data, the C-Motif algorithm successfully reports a relatively complete set of of conditional phosphorylation motifs efficiently. -
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ARDEN
Specificity Control for Read Alignments Using an Artificial Reference
...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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...The first module in the project was the "ePrescribing application"; certified by RxHub and SureScripts back in 2007. New implementation needs to "re-certify" with SureScripts (which should not be much of a problem) Work on eLabs (using ELINCS, LOINC etc.) is being considered as participants join the project become available. The HL7 RIM allows for eImaging applications, eConsults applications, eReferrals applications, etc. Applications work independently, but through HIE, results come back to the provider to see it in its "CPOE Section or Module" Requires licensing of the MediSpan Drug Database for ePrescrib
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TreeLiker
TreeLiker is a collection of fast algorithms for working with complex
...The algorithms included in TreeLiker are unique in that, in principle, they are able to search given sets of relational patterns exhaustively, thus guaranteeing that if some good pattern capturing an important feature of the problem exists, it will be found. In experiments with real-life data, the algorithms were shown to be able to construct complete non-redundant sets of patterns for chemical datasets involving several thousands of molecules as well as for comparably large datasets from genomics or proteomics. The included relational learning algorithms are tailored towards so-called tree-like features for which some otherwise very hard sub-problems (NP-hard) become tractable. -
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Javamony
A Student's Approach to the Phylogenetic Problem
Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem. Javamony is invoked as follows: java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ... Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve fundamental problems in phylogenetics. ... -
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Pysimony
A Pythonic Implementation of Parsimony Inference of Phylogeny
...An unlikely-to-be-the-most-parsimonious tree is printed upon completion in basic Newick tree format. As all parts of the program are the original work of a beginner programmer, this may represent one of the worst approaches to solving the phylogenetic problem. I have clearly avoided object-oriented programming. Nevertheless, I distribute this imagining it might someday be slightly educational or at least provide a laugh at the pathetic attempt it makes to reinvent the wheel -
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pyBioImage
Biological Imaging Software suite
The pyBioImage is a python a python based biological imaging suite tailored to the problem of finding Germinal Center "spots" within multidimensional microscopy images as it is described in the research paper: "Software tool for 3D extraction of germinal centers", by David N. Olivieri, Merly Escalona and Jose Faro. -
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This tool is designed to solve generalized pattern matching problem, by which we only find a set of sub-patterns, ignoring the gaps in between the sub-patterns. This tool is extremely fast and also has good tolerance to errors.
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Gene regulation is an important current matter of research. TFBS predictions will help understanding it. A problem with common tools are many putative false positives and a lack of visualizing TFBS evolution. This tool aims to solve these problems.
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FORce based Cluster Editing (FORCE) is a Java software heuristically solving the graph cluster editing problem on weighted edges using BLAST E-values. It further provides a training mode for heuristic parameter estimation.
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It moves by itself inside networks like virus infection & plagues, it is being written to solve computer virus problem drastically and responsibly. It is legal, free and open for public domain to improve W3 ICT Security.
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Set of Java packages to apply Genetic Algorithms to any kind of problem. Various genetic operators are implemented and an example shows of how the system could be applied to digital circuit evolution.
