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Showing 9 open source projects for "can"
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Gemi
PCR primers / probes design from multiple & degenerate sequences
Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR (qPCR, rt-PCR, etc.), and Sanger sequencing. Gemi can parse large dataset of sequences efficiently. Python source code is available upon request. Milestone: The tool reached about 3000 downloads sine 2012. Article Gemi: PCR primers prediction from multiple alignments. ... -
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ShuffleFastaSeq
This application can be used to shuffle sequences in FASTA format.
...The art of computer programming: seminumerical algorithms. 3rd ed. Boston: Addison-Wesley; 1997). The input file contains one or more sequences in FASTA format. The number of shufflings (n) for each sequence can be set; by default n is 100. The output file contains n shuffled copies in FASTA format for each input sequence. For example (n=3): Input file: >a ACGGT >b GCCCATTC Output file: >a TCGAG >a CGAGT >a TGCGA >b CACTCCGT >b CCCGTATC >b CCTTCAGC -
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Shoal
A lot of fish in a shoal, in a gigantic scientific ocean.
...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 needs grownup I'm just a student in the university, and the shoal shell just in its begining, if you have any idea about shoal, please contact me from xie.guigang@gmail.com. The Shoal shell needs your professional advice. Try get some help (if you want build the shoal library by yourself): https://sourceforge.net/p/shoal/wiki/Shoal%20Developer%20Guide/ -
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This project hosts the 'Simulation Tool', an extensible, interactive environment for carrying out simulation experiments of SBML models. This project can use RoadRunner or SBW enabled simulators to carry out simulations.
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Online Signature Verification
Real time signature verification using MATLAB and C#
Online Signature Verification technology requires primarily a digitizing tablet and a special pen connected to the USB port of a computer. An individual can sign on the digitizing tablet using the special pen regardless of his signature size and position. The signature is characterized as pen-strokes consisting x-y coordinates and pressure with the data being stored in a signature database. Dynamic time warping (DTW) and quadratic discriminant analysis (QDA) is used to get results where the system accepts 2% of forged signatures and rejects 5% of true signatures -
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PeptideManager_LRNO
Unique Peptide Sequence Finder (host background (xenografts) friendly)
PeptideManager is aimed to help the pre-selection of unique peptide sequences for the design of targeted proteomics approaches. Its main advantage is to allow the presence of a host/background proteome (e.g., xenograft samples) during this peptide sequences selection. PeptideManager can build peptide sequences databases from various public repository (SwissProt/Trembl/UniProt, RefSeq, IPI) and various proteases. For any use, please refer to the publication: doi: 10.3389/fgene.2014.00305 http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00305/abstract -
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
BiSA is a bioinformatics database resource that allows investigators to run a number of overlapping genomic region analyses using their own datasets, or against the pre-loaded Knowledge Base. Analysis results can be restricted to a chromosome; the minimum base pair overlap in two sets or maximum distance between regions can be set; as can the maximum allowed distance between region centres. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are nearby; regions that are not overlapping; average region sizes. ... -
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xemload
Generate XEML documents from your CSV metadata records
XEML is a language that is used to represent and design plant growth experiments. Using a wizard like interface, XemLoad allows users to transform the environmental conditions records stored as CSV files into XEML files. The experiment can either be an existing XEML document or it can be created from scratch using XemLoad. Environmental Conditions must be paired with dedicated ontologies terms, the default one being the embedded XEO (Xeml Environmental Ontology). XEO was also redesigned as part of this projet to get rid of inconsistencies and redundancy that existed in the original version. -
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The goal of EPT is to get track representations from the clipboard (put there by Ethovision) and to automatically save the serie of images while incrementing a value in their filename.
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