Search Results for "e-root"
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Showing 35 open source projects for "e-root"
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GelJ
GelJ is a Java program for the analysis of DNA gel fingerprints images
...Some of the outstanding features of GelJ are functionality for accurate lane- and band-detection, several methods for computing migration models and generating dendrograms, comparison of banding patterns from different experiments, and database support. Citing GelJ: J. Heras, C. Domínguez, E. Mata, and V. Pascual. GelJ – a tool for analyzing DNA fingerprint gel images. BMC Bioinformatics 2015, 16:270 http://doi.org/10.1186/s12859-015-0703-0. You can see more information about GelJ in https://sourceforge.net/p/gelj/wiki/Home/ Several videos explaining the use of GelJ are available in https://sourceforge.net/p/gelj/wiki/Videos/ Please address any question or comment to joheras at gmail.com -
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ANDTool
Analysis Nuclei DAB (AND) Tool
...USER MANUAL: see the specific PDF available in the Files section. REQUIREMENTS: MATLAB R2017b and Image Processing Toolbox 10.1 or later versions. MAIN CONTACT: Filippo Piccinini (E-mail: filippo.piccinini85@gmail.com) -
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e-Species
A taxonomically intelligent biodiversity search engine
This is a pure Python CGI-based implementation of a taxonomically intelligent species search engine. It searches biological databases for a taxonomic name. The search is done "on the fly" using web services (SOAP/XML) or URL API's. -
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AntibiogramJ
AntibiogramJ is a Java program for the reading of antibiogram-images
AntibiogramJ is a Java program for the identification, measurement and categorisation of inhibition zones in antibiogram images captured with any device that incorporates a camera (including digital cameras and mobile phones). Citing AntibiogramJ: A. Alonso, C. Domínguez, J. Heras, E. Mata, V. Pascual, C. Torres, and M. Zarazaga. AntibiogramJ: a Tool for Analysing Images from Disk Diffusion Tests. Computer Methods and Programs in Biomedicine 143:159-169. 2017. DOI: http://dx.doi.org/10.1016/j.cmpb.2017.03.010 You can see more information about AntibiogramJ in https://sourceforge.net/p/antibiogramj/wiki/Home/ Several videos explaining the use of AntibiogramJ are available in https://sourceforge.net/p/antibiogramj/wiki/Videos/ AntibiogramJ includes now the EUCAST v.9.0. ... -
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Root Phenotyping Suite
Three different software tools for phenotyping plant root images
RootAnalyzer is a fully automated tool, for efficiently extracting and analyzing anatomical traits from root-cross section images. RootAnalyzer segments the plant root from the image's background, classifies and characterizes the cortex, stele, endodermis and metaxylem, and produces statistics about the morphological properties of the root cells and tissues. RTipC is a system for the fully automated detection and classification of root tips in root images obtained either by 2d flat bed scanning or by 3D digital camera imaging. ... -
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The source code has been migrated and is now hosted on Github: https://github.com/jenetics/jenetics Jenetics is an advanced Genetic Algorithm, Evolutionary Algorithm and Genetic Programming library, respectively, written in modern day Java. It is designed with a clear separation of the several algorithm concepts, e. g. Gene, Chromosome, Genotype, Phenotype, Population and fitness Function. Jenetics allows you to minimize or maximize the given fitness function without tweaking it. In contrast to other GA implementations, the library uses the concept of an evolution stream (EvolutionStream) for executing the evolution steps. Since the EvolutionStream implements the Java Stream interface, it works smoothly with the rest of the Java Stream API. ...
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LOCUST
Custom Sequence Locus Typer
A Custom Sequence Locus Typer for Classifying Microbial Genotypic and Phenotypic Attributes. Publication: Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G. LOCUST: A Custom Sequence Locus Typer for Classifying Microbial Isolates. Bioinformatics (Oxford, England). 2017 Jan 27; https://www.ncbi.nlm.nih.gov/pubmed/28130240 -
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LMAP
Lightweight Multigene Analyses in PAML
Maldonado E, Almeida D, Escalona T, Khan I, Vasconcelos V and Antunes A (2016) LMAP: Lightweight Multigene Analyses in PAML. BMC Bioinformatics, 17:354. doi: https://doi.org/10.1186/s12859-016-1204-5 -
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CuiTools (Coo-e Tools) is a freely available package of Perl programs for unsupervised and supervised word sense disambiguation experiments. The name CuiTools comes from the Concept Unique Identifiers (CUIs) found in the Unified Medical Language System.
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Mass Difference Calculator
Mass Difference Calculator with a Graph for MassLynx data
A Mass Difference Calculator with a graph for MassLynx. Bring in a text file with reference masses and then paste in or browse in another file with a list of mass/intensity pairs. Then look at the best matching points and see what the difference between reference and data comes out as. This is a companion app to ResCalc3 -
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Community Detection Modularity Suite
Suite of community detection algorithms based on Modularity
... - Main suite containing three community detection algorithms based on the Modularity measure containing: Geodesic and Random Walk edge Betweenness [1] and Spectral Modularity [2]. Collaborator: Theologos Kotsos. [1] M. Newman & M. Girvan, Physical Review, E 69 (026113), 2004. [2] M. Newman, Physical Review E, 74(3):036104, 2006. [3] B. Ball et al, An efficient and principled method for detecting communities in networks, 2011. The suite is based upon the fast community algorithm implemented by Aaron Clauset <aaron@cs.unm.edu>, Chris Moore, Mark Newman, and the R IGraph library Copyright (C) 2007 Gabor Csardi <csardi@rmki.kfki.hu>. ... -
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ChIP-RNA-seqPRO
ChIP-RNA-sequencing-processing (ChIP-RNA-seqPRO)
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic,... -
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PRIMUS
Pedigree Reconstruction and Identification of a Maximum Unrelated Set
...For example, when there are two equally sized maximum sets of unrelated individuals in a network, PRIMUS can preferentially select the set with more affected individuals. Subscribe to the PRIMUS-Users e-mail list for notifications of updates and new versions. Relevant software: http://students.washington.edu/jeanm5/Simulate_IBD_Python.ta -
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LipidWrapper
Create lipid-bilayer models of arbitrary geometry.
...When building large-scale models of whole subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature are essential. LipidWrapper, written by Jacob Durrant in the lab of Rommie E. Amaro, is capable of creating curved membrane models with geometries derived from various possible sources, both experimental and theoretical. We are hopeful that this utility will be a useful tool for the computational-biology community. -
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Marta
Cancer Registry Web Application
Marta è una web application nata per aiutare i Registri Tumori. Accesso sicuro alle informazioni, tool di importazione, algoritmi di analisi e molto altro. Ma ho bisogno di una mano...da solo non ho abbastanza tempo ! Se volete aiutare, contattatemi su: - **gmail/hangout** dangeloantonio179@gmail.com - **skype** sickpuppies73 Più ne siamo e meglio è ! -
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Pyntrez
Command-line, Entrez, NCBI e-utilities client, written in Python
Command-line, Entrez, NCBI e-utilities client, written in Python; developed for Linux -
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Pyntrez NCBI Database Client
Command-line, Entrez, NCBI e-utilities client, written in Python
Comman-line client to Entrez, e-utilities, written in Python, developed for Linux -
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IMPACT_S
Integrated Multiprogram Platform Analyze & Combine Tests of Selection
Maldonado E, Sunagar K, Almeida D, Vasconcelos V, Antunes A (2014) IMPACT_S: Integrated Multiprogram Platform to Analyze and Combine Tests of Selection. PLoS ONE 9(10): e96243. doi: https://doi.org/10.1371/journal.pone.0096243 -
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WebChemViewer
A simple program for sharing molecular structures with associated data
...The output can also be easily incorporated into existing web pages. WebChem Viewer is released under the FreeBSD license. It was created by Jacob Durrant, a post-doc in the lab of Rommie E. Amaro. -
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EASER
Ensembl Easy Sequence Retriever
Maldonado E, Khan I, Philip S, Vasconcelos V, Antunes A (2013) EASER: Ensembl Easy Sequence Retriever. Evolutionary Bioinformatics, 9:487-490. doi: https://doi.org/10.4137/EBO.S11335. -
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SBEToolbox
Systems Biology and Evolution Toolbox (SBEToolbox).
.... ******************************************************************************************************************************** PROJECT MIGRATED TO GITHUB FOR FUTURE UPDATES: https://github.com/biocoder/SBEToolbox/releases ******************************************************************************************************************************** Reference ( In Press ): ================= Konganti K, Wang G, Yang E, Cai JJ* (2013). SBEToolbox: a Matlab toolbox for biological network analysis. Evolutionary Bioinformatics, 8:1-15 -
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cosmos-fp7
COordination of Standards in MetabOlomicS
COSMOS (Coordination of Standards in Metabolomics) brings together European data providers to set and promote community standards that will make it easier to disseminate metabolomics data through life science e-infrastructures. The sf.net project is home for tools and data which don't have another upstream. -
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Pop-seq
Population simulator to solve next generation sequencing questions
...Combined with the Seq-sim tool you can generate pooled or bar-coded next generation sequencing biased outcomes. This tool were used to solve reappearing question in a experimental design (e. g. of how many plants or sequencing depth is advisable in a back crossed or out crossed scenario ) -
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smooth
Wavelet smoothing in a data stream
...The 'smooth' utility applies such smoothing using the wavelet algorithm. This implementation of wavelet smoothing was optimized for use in a data stream. It was adapted from HMMSeg Wavelet.Java by Thomas E. Wilson, University of Michigan. HMMSeg Wavelet.Java was written by Andrew Hemmaplardh, University of Washington. http://noble.gs.washington.edu/proj/hmmseg/ Unsupervised segmentation of continuous genomic data, Bioinformatics 2007 23:1424-1426 See the above references for a more thorough description of the principles behind wavelet smoothing. -
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DyMMM
Dynamic Multispecies Metabolic Modeling framework
...R. (2011). Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. The ISME journal. Zhuang, K., Ma, E., Lovley, D. R., & Mahadevan, R. (2012). The design of long-term effective uranium bioremediation strategy using a community metabolic model. Biotechnology and Bioengineering.
