Search Results for "draft"
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Showing 21 open source projects for "draft"
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Prokka
Rapid prokaryotic genome annotation
Prokka is a command-line software tool for rapid annotation of prokaryotic genomes (bacteria and archaea). Given a FASTA file of contigs, it predicts genes, rRNAs, tRNAs, and other functional elements, then assigns functions by comparing to reference protein databases and HMM profiles. It outputs GenBank, GFF, and other formats compatible with downstream tools and genome browsers. Prokka handles common complications—overlapping ORFs, frameshifts, alternate start codons—while providing... -
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libCIGI
C++ Library for the Common Image Generator Interface
libCIGI (library for Common Image Generator Interface) is a lightweight header only library that provides interfaces for communication between CIGI hosts and image generators. Currently versions 3.0, 3.2 and 3.3 are supported as well as support for the *draft* V4.0 CIGI standard. Additional functionality to the base packet interfaces is provided through external classes so that to the packet headers have no further dependencies. Packet processing is kept simple and a couple of simple helper functions / classes are provided in CIGIGeneric.h and some other headers to support this. Helpers are provided for version interpretation and conversion of packet parameters to text. ... -
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KDIS
DIS(IEEE 1278.1) Fully Implemented in C++
A complete open source implementation of DIS (Distributed Interactive Simulation) in C++. 1278.1 and 1278.1a are fully implemented including enumerations. Includes several utility classes to help with developing your DIS app. DIS 7 work is ongoing. -
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SDC
SDC facilitates development of dist. systems of medical devices.
...It is based on the upcoming SDC standard, which is specified by the IEEE in IEEE Std 11073-20702-2016 (Point-of-care medical device communication Part 20702: Medical Devices Communication Profile for Web Services), IEEE Std 11073-10207-2017 (Point-of-care medical device communication Part 10207: Domain Information and Service Model for Service-Oriented Point-of-Care Medical Device Communication), and P11073-20701 (IEEE Draft Standard for Service-Oriented Medical Device Exchange Architecture & Protocol Binding). The SDC standard has the goal to meet increasing demand for medical device interoperability in an Integrated Clinical Environment (ICE), see also ASTM F2761-1:2009. OpenSDC is not intended to be used in clinical trials, clinical studies, or in clinical routine. -
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Wuweido 3D CAD
Free 3D Mobile CAD
...Wuweido is powered by OPEN CASCADE. OPEN CASCADE is an incredible powerful geometry kernel innovating quickly. Wuweido is inspired by CAD Assistant. Modeling features: 1. Draft creation tools: Line, Poly Line, Arc, Spline, Circle, Ellipse, Rectangle, Regular Polygon. 2. Primitive Solid creation tools: Box, Cone, Truncated Cone, Cylinder, Sphere, Torus, Wedge, Truncated Wedge, Pyramid, Truncated Pyramid. 3. Sweep modeling tools: Extrude, Revolve, Loft, Pipe, Path 4. Boolean operation tools: Intersect, Subtract, Union, Xor, Fuse 5. ... -
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PBSuite
Software for Long-Read Sequencing Data from PacBio
.... ----- PBJelly ----- Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768 PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. ----- PBHoney ----- Read The Paper http://www.biomedcentral.com/1471-2105/15/180/abstract PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). ... -
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iCAS - An Illumina Clone Assembly System
An Illumina clone assembly system using SOAPdenovo and ABySS
...With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting in near perfect pre-assembly reads. Contigs are generated using different assembly algorithms and then merged together to achieve longer continuity. Re-aligning all the reads back to the draft contigs and recalibrating each sequence base achieves a final consensus. Using finished clones for QC, the pipeline is able to obtain assemblies with clone coverage of 99.7% and consensus base quality of Q39. Developed at the Wellcome Trust Sanger Institute. -
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ENLY
Bioinformatic tool to improve draft genome assemblies by closing gaps
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hbgm
'Hierarchical Bond Graph Modelling of Biochemical Networks'
... (3) Department of Mathematics and Statistics, University of Melbourne, Victoria 3010, Australia. (4) School of Medicine, University of Melbourne, Victoria 3010, Australia Draft paper available at http://arxiv.org/abs/1503.01814 -
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FIAP
Fully Integrated Annotation Pipeline
...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 users to annotate, for example, draft genome contigs or different genomes concatenated in multi-fasta file in a single step. FIAP works on all UNIX-like operating systems (tested on Ubuntu 14.04 LTS and Mac OS 10.9.4). -
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VIGOR3
Annotation of Viral Genomes
VIGOR is a tool for annotating coding genes in viral genomes. It was developed by Jeffrey Hoover and Shiliang Wang for The JCVI Genomic Sequencing Center for Infectious Diseases (GSCID). http://www.biomedcentral.com/content/pdf/1471-2105-11-451.pdf contact: Jeff Hoover 301-540-7858 jefhv@aol.com -
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The Blast2SNP is able to pick out synonymous, non-synonymous mutations and indels from draft assembly sequences by performing BLAST search against the reference ORF sequences.
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MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
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Pamvotis is a Wireless LAN Simulator for all the current physical layer extentions of the IEEE 802.11 (IEEE 802.11 a/b/g) standard and for the IEEE 802.11e Draft for Quality of Service in WLANs.
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vcif is an open source software for validation of Crystallographic Information Files. It supports lexical, parser and dictionary validation (DDL 1 and 2 are fully supported, DDLm draft partially supported)
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SimpleWFS is a 100% Java servlet implementation of the draft OGC standard Web Feature Service (WFS) Simple. This is a Web service interface whose goal is to specify a common, minimal feature set for geospatial-temporal data access.
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This software collection is for a DNA sequencing laboratory. It is used to design closure/finishing reactions following a shotgun sequencing experiment. It requires a draft assembly composed of contigs and scaffolds.
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Free cross-platform viewer for seismic data in SEG-Y format (Revision 1 draft 6 and its modifications).
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A dialect of XUL implementing most of Mozilla XUL's Fourth Draft. XML User Interface Language (XUL) is a method for easily creating GUI applications. Lux XUL supports Python scripting via Jython 2.1.
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Software to act on a robotic arm, the draft also contains the layout of the arm and explanations to build it.
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