Search Results for "bio process" - Page 2
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Showing 58 open source projects for "bio process"
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dna-bison
Bisulfite alignment On Nodes of a cluster
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2. Multiple compute nodes are not absolutely required, but will make the alignment process faster. Further details available on the Wiki page. Help also available on SEQanswers (http://seqanswers.com/forums/showthread.php?t=31314) or by creating a ticket here. You can now track the... -
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FIAP
Fully Integrated Annotation Pipeline
FIAP (Fully Integrated Annotation Pipeline) is a fast bacterial genome multithreading annotation pipeline written in Perl that detects genes coding for proteins, tRNAs, and rRNAs (5S, 16S and 23S). FIAP also allows users to include an infinite number of custom databases. This feature is extremely valuable because it allows users to add a personal “flavor” to the annotation and optimize the process for a specific bacterial genome. FIAP can annotate single and multiple sequences, which allows... -
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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... -
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IQuant
A pipeline for quantitative proteomics based upon isobaric tags
IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by... -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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basecv
BCV is DNA base caller with vocabulary
The Base Calling with Vocabulary (BCV) software package is intended for analysis of direct (population) sequencing chromatograms using known vocabulary sequences similar to the target DNA. The current version of BCV can only process chromatogram files obtained on Applied Biosystems capillary sequencing machines (ABIF file format). -
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GraFIX is a software and a method to detect fixations in low and high quality data, consisting of a two-step process in which eye-tracking data is initially parsed by using adaptive velocity-based algorithms, before it is hand-coded using the graphical interface, allowing accurate and rapid adjustments of the algorithms' outcome. GraFIX is released under the GPLv3 public license (http://www.gnu.org/licenses/). Please cite as: Saez de Urabain, I.R., Johnson, M.H., Smith, T.J., (2014)...
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A bioinformatics tool to PRe-process and show INformation of SEQuence data. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.
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The goal of this project is to combine different sources of information as well as methods to help in the process of gap closing / genome finishing in high throughput sequencing.
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CADET
Chromatography Analysis and Design Toolkit
...The CADET framework also comprises a MATLAB interface and standard routines for parameter estimation, process optimization and experimental design. CADET is freely distributed as a contribution to the scientific community. If you find it useful for your own work, we would appreciate acknowledgements of the CADET software and citations of our papers: http://doi.org/10.1016/j.compchemeng.2010.03.008 http://doi.org/10.1016/j.compchemeng.2018.02.025 -
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primeScaff is intended to automate the sometimes tedious process of manually designing specific primer pairs around gaps of genomic scaffolds and speedup the genome finishing stage of a genome sequencing project. It incorporates de-novo repeat finding using RECON to avoid as much as possible designing primers in repetitive regions and offers the possibility to easily fine-tune the primer design options using primer3. It outputs the repeat, gap and primer annotations in gff2 and gff3 to...
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DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.
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Onco-STS
A web-based Laboratory Information Management System
Onco-STS is a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centers, platforms, data locations,... -
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CUO
Codon Usage Optimizer
CUO is a GUI-based multiplatform software written in Java. It is open source and built with a user/developer-friendly structure. The main function of the software at the current development stage is to optimize genes to be transformed into the Chlamydomonas reinhardtii chloroplast genome although it can be used to optimize genes into other hosts as well. The main tool in CUO, Moptimizer, introduces a semi-automatic way of gene optimization which provides more flexibility and accuracy during... -
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The Self-Organizing Map Maker for Education and Research. Features include 3D-visualization of the training process, various 2D and 3D map topologies, easy extensibility to additional topologies.
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u/sbmv2012
Taxonomy assignment of metazoans using a python based pipeline
The aim of this project is to create an automated pipeline for taxonomic assignment of DNA sequences obtained from environmental samples. We develop a series of python scripts to process the raw sequence data obtained from benthic environmental samples and to taxonomical assignment of these sequences and finally to integrate all data in a relational database. -
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Primer Design Tool
Design PCR primers
A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them. -
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This project (osgi4ami-tecnodiscap) comes from the branch revision-3 of the osgi4ami project as a name standardization process, following osgi4ami-monami project creation. This project becomes the Universidad de Zaragoza (Tecnodiscap) Implementation.
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Linking Yabi with RDA
This software system enables publication of YABI workflows to the RDA.
Modern life science research requires bringing together Biology and Information technology. To help make this process easier, the CCG has developed YABI, an Internet based workflow application that is aimed at biologists who wish to conduct bioinformatics analysis. YABI integrates bioinformatics tools and data via an intuitive workflow creation and management environment. YABI can be used to access the NCI-SF in Bioinformatics and the tools available through the Embl Australia EBI mirror... -
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QUASR
Cross-platform NGS processing and analysis pipeline in Python
QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is... -
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ASpipe is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments. It requires unix bash, perl 5.0+ with DBI module and MySQL5.0+ to run properly.
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PerlPrimer is a GUI application written in Perl that designs primers for standard PCR, bisulphite PCR and Real-time PCR (QPCR). It aims to automate and simplify the process of primer design.
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A plugin for the VANTED system, called Glyph-based Link Exploration of Pathways (GLIEP). It helps to guide the navigation and exploration process of interconnected pathway visualization as well as insight into the overall interconnectivity.
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BigRedBin is a web-based tool designed to pre-process metabolomics data generated by a mass spectrometer in an attempt to increase the signal-to-noise ratio. This is accomplished by using information from multiple technical replicates.
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ChiBE
Chisio BioPAX Editor
ChiBE (Chisio BioPAX Editor) is an open source pathway editor for biological pathways in BioPAX format. ChiBE converts BioPAX graphs into process diagrams where complexes and compartments are represented with compound nodes. !!! For latest version, please see !!! http://code.google.com/p/chibe -
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