Search Results for "bed" - Page 2
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Showing 73 open source projects for "bed"
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RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
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TinyCog
Cognitive architecture with a focus on self-models
TinyCog is a cognitive architecture (perception, action, reasoning, planning, and language) with a focus on representing "self-models" (physical, capabilities, intentions, social, historical, "cognitive stream") in order to implement social reasoning and collaborative planning in a "hunter domain" test bed. We use Prolog, RDF Triples, Description Logic and a HTN-Planner as base technologies. -
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OWASP Security Shepherd
Web and mobile application security awareness/training platform
The OWASP Security Shepherd project enables users to learn or to improve upon existing manual penetration testing skills. Utilizing the OWASP top ten as a challenge test bed, common security vulnerabilities can be explored and their impact on a system understood. The by-product of this challenge game is the acquired skill to harden a player's own environment from OWASP top ten security risks. The modules have been crafted to provide not only a challenge for a security novice, but security professionals as well. ... -
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WigMaker
make wiggle file from bed file for ChIP-seq samples
This application takes bed file(or gzip bed, with .gz extension) as input, it creats a single file or a fold like 'wigs for xxx' in which the chromosome separated wiggle files will be saved. Users can set the wigextend value and step value for the output wig files. By default, they are 200 and 25. The application requires a lot of memory (about 2GB) -
Enterprise-grade ITSM, for every businessFreshservice is an intuitive, AI-powered platform that helps IT, operations, and business teams deliver exceptional service without the usual complexity. Automate repetitive tasks, resolve issues faster, and provide seamless support across the organization. From managing incidents and assets to driving smarter decisions, Freshservice makes it easy to stay efficient and scale with confidence.
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jChIP
Graphical environment for exploratory ChIPSeq data analysis
...In addition it computes statistics of the number of loci/positions containing specified amount of tags. jChIP is able to load data in several common formats (SAM, BAM, WIG, BED, Bowtie) and download loci definitions directly from the Ensembl database. http://www.biomedcentral.com/1756-0500/7/676 -
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Auto Primer3
Automatically design primers to genes/coordinates using primer3.
PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/autoprimer3) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/autoprimer3/releases/latest). AutoPrimer3 retrieves gene information, DNA sequences and SNP information from the UCSC genome browser and uses primer3 to automatically design primers to genes or genomic coordinate targets. Primers may be designed using information from any of the UCSC hosted genomes... -
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ImageTerrier is an open-source, scalable, high-performance search engine platform for content-based image retrieval applications. The platform provides a comprehensive test-bed for experimenting with image retrieval techniques.
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Zalarm
Alarm Clock with a couple of nice extra features. Wake up your way.
...Or maybe you are the kind that prefers the more soft and sensitive alarms. With Zalarm this is all up to you. The reason for adding notes to the alarm is simple. Maybe by the time you go to bed you have a brilliant idea, or there is something you have to remember by the time you wake up. This feature let you get reminded of this. When the alarm goes off, you will in addition to the alarm get a pop-up message. The message contains your predefined notes. This however is completely optional. Enjoy! -
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Athus
Manage, merge, filter and convert population genetics data
This project assists you in performing population genetic analyses by taking over the ugly, boring and error-prone data manipulation steps. Starting from well specified input formats VCF, BED and FASTA and a unique configuration file describing data (f.e. from SNP-arrays or sequencing) as well as filtering one can create standard POPGEN formats like Eigenstrat, PEDMAP (PLINK), Treemix ... In addition there are several utilities for * generating VCF from SNPArray data (NCBI - GEO, Illumina call files) * work with genetic maps ... -
Gemini 3 and 200+ AI Models on One PlatformBuild, govern, and optimize agents and models with Gemini Enterprise Agent Platform.
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It is a framework for testing various revisitation algorithms on real datasets. Some algorithms have already been implemented and are available for testing. Additional algorithms can be added by users and evaluated on this test bed.
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CADET
Chromatography Analysis and Design Toolkit
We have moved to GitHub: https://github.com/cadet The Chromatography Analysis and Design Toolkit (CADET) is developed at the Institute of Bio- and Geosciences 1 (IBG-1) under supervision of Prof. Eric von Lieres. The core of the CADET software is a fast and accurate solver for the General Rate Model (GRM) of packed bed liquid chromatography. The CADET solver covers a wide range of GRM variants, combining different transport and binding models with state-of-the-art mathematical algorithms and scientific computing techniques. The CADET framework also comprises a MATLAB interface and standard routines for parameter estimation, process optimization and experimental design. ... -
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indicator-hosts-up
Panel Indicator to interact and monitor hosts
It is an easy and handy way for home or small offices where nowadays we have many hosts (pcs, routers, smartphones, NAS, media centers, wi-fi intruders, etc) and we want to know what is up and interact with them. This was born as many others from my need to turn on/off a computer in another room or see what is up before going to bed or be alerted by some intrusion in my local net via wi-fi. It needs a lot of improvements and I hope the community can help. New hosts are discovered via /etc/hosts and nmap but can be added manually too. -
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CKSauthorer
Work in progress K99/R00 project at Mayo and Northwestern
...This project investigates the feasibility of using a novel text mining based informatics approach to semi-automate the management of a clinical knowledge system, using UpToDate as the test bed. Although the methods will be applicable to any clinical knowledge system and any topic, they will be evaluated using two important test topics from cardiology – congestive heart failure and atrial fibrillation. While the existing content of UpToDate is private, the methods and the code we develop to assist in generating the content are being released incrementally. ... -
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ligth-genome-view
small genome viewer local wxWidget c++
...I am a newbie in bioinformatics. Hope this will give people help when build bio-GUI project using c++. This software is used to view genome including many type files,like bed,gff,gtf,vcf,fasta,bam. -
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Locanda
Booking management system for hotels, bed&breakfasts, guesthouses
Locanda is an innovative booking management system designed for any touristical structure such as hotels, bed and breakfasts, guesthouses, farmhouses. Featuring a user-friendly and dynamic web interface, Locanda allows a seamless management of all the resources an owner has to control: Bookings, Rooms, Room Types, Guests, Extras, Price Lists, Seasons, Conventions. It is a system developed by the Open Source Lab c/o Sardegna Ricerche, Sardinia, Italy. -
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HPeak
A HMM-based algorithm for defining enriched regions from ChIP-seq data
...Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites. Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -pe TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -isize 200 -r 100 -pec (if control is PE) -ann -wig -seq –interfiles note: 1. Default species is HUMAN. ... -
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GenOO-HTS
A Modern Perl Framework for High Throughput Sequencing analysis
GenOO-HTS [jee-noo] is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools. The primary aim of GenOO-HTS is to make simple HTS analyses easy and complicated analyses possible. GenOO-HTS models biological entities into Perl objects and provides relevant attributes and methods that allow for the manipulation of high throughput sequencing data. Using GenOO-HTS as a core development module reduces the overhead... -
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monoDevPrjs
Idea bank for projects using MonoDevelop
Not much more to say. This is just a test bed for MonoDevelop projects which might later take on a life of their own. The first project here is to make a productivity / project administration program, which I am calling RBMhelper. When it becomes alpha stage, I'll move it over to my other project repository with that name. "miniTimer" is a basic count up /down timer. -
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iPiG
Integrating PSMs into Genome browser visualisations
iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers. For more details about iPiG and it's functionallity, please see "iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations" Mathias Kuhring and Bernhard Y. Renard (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0050246) -
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DAiict Mesh Network (DAMN)
DAMN is an attempt to create a mesh network in DAIICT campus.
DAMN, as a mesh network will allow free communication inside the campus at DAIICT. Telephony, file sharing and other LAN applications can now be used on the go with the mesh network acting as a Wireless LAN. DAMN will also act as a test bed for future research in DAIICT. -
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A test bed for experiments on achieving and enhancing technical interoperability between and with help of Open Source middleware components. Developed under QualiPSo (http://www.qualipso.org), WP3.1
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wificolab
SW applications for the RF test-bed built at UTB Zlin
The web application providing user management, measurement reservations, and measurements. Wificolab communicates with the R&S FSV analyzer using the VXI11 protocol, It can setup the FSV using a setup template. An user can then run the measurement directly from wificolab web and store the resulting data in the database. The data are presented in the form of graphs. The measurement results can be shared with other users and can be compared graphically – it is possible to display several... -
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Criminal minds revealed and played. Criminal acts in all sorts of places with great animation and daily updated by Developer Fontella Moneet Farrar.
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ZaK is a property management system for hotel and bed and breakfast. It's developed with python (twisted) and html5 (jquery and web sql database). It allows to manage rooms, reservations and quotes.
