Search Results for "platform-tools"
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Showing 156 open source projects for "platform-tools"
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SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools
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Prokka
Rapid prokaryotic genome annotation
...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 customizable databases so researchers can bias domain or strain-specific annotations. The pipeline is optimized for speed, using multithreading and caching to annotate large microbial genomes in minutes. ... -
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Th3inspector
Best Tool For Information Gathering
Th3Inspector is a Perl- and shell-based, all-in-one information-gathering toolkit built to quickly enumerate public and semi-public data about targets (domains, IPs, phone numbers, mail servers, etc.). It exposes a single command-line entrypoint (Th3inspector.pl) with many switches for common reconnaissance tasks — examples include website info, whois, MX lookup, geo-IP, subdomain discovery, CMS detection, port scanning, and Cloudflare real-IP resolution — so a user can chain many checks... -
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WxTools (Weather Data Tools)
This package collects Fine Offset and Oregon Scientific weather data.
WxTools (Weather Data Tool Suite) is a collection of software for collecting and displaying weather data from various weather stations. The software works with the Fine Offset WH290 and similar models (including clones such as the Pro-Signal PSG04173). It also works with the Oregon Scientific WMR180 weather station (and probably similar models such as the WMR88 and WMR100) as well as the older WMR928. Sample weather data is provided. -
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Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format. -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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Monte Carlo eXtreme (MCX)
Physically accurate and validated GPU ray-tracer
MCX is a GPU-accelerated, general-purpose, physically-accurate and feature-rich 3-D light transport simulator. It is one of the fastest simulators because it can use tens of thousands of GPU threads to simulate photons in parallel. -
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contools
console tools, batch scripts, vbs scripts
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Bridge Designer and Contest
A national virtual bridge engineering contest for kids of all ages.
...The new support channel is bridgedesignerteam@gmail.com The national contest is no longer active. Several regional contests exist worldwide. The new Bridge Designer includes tools for contest support. -------------- A national virtual bridge engineering contest with prizes for middle and high school kids, grades 6 to 12, but anyone can enter for fun. Based on the award-wining Bridge Designer client software, now open source through this project. Web site infrastructure supports worldwide participation in qualifying and semifinal rounds with a tiny administrative staff. -
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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DkIT Bridge Designer
Dundalk Institute of Technology Virtual Bridge Design Competition
The DkIT Bridge Designer will provide you with a realistic introduction to engineering through an authentic, hands-on design experience. This software provides you with the tools to model, test, and optimize a steel highway bridge, based on realistic specifications, constraints, and performance criteria. Supported by Dundalk Insititute of Technology and All-Island Funds, this is a virtual bridge designer that allows kids of all ages learn about engineering and compete with their classmates! -
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gputils is a collection of tools for Microchip PIC microcontrollers. Its goal is to be fully compatible with Microchip's tools, MPASM, MPLINK, and MPLIB.
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CSI-Math-Notation-PostfixInfix
Perl Lib Math Notation
* Introduction: - This Module is a Library based Perl code. - The library provide: - Convert INFIX expressions to POSTFIX; - Convert POSTFIX expressions to INFIX and; - Perform POSTFIX context validations. - Context validation can be implemented in item selection routines or data context validation, when it is possible to identify data to be selected or ignored in some data analysis process. * NOTE: - Before any implementation, we recommend details in WIKI... -
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UrJTAG aims to create an enhanced, modern tool for communicating over JTAG with flash chips, CPUs, and many more. It is a descendant of the popular openwince JTAG tools with a lot of additional features and enhancements.
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not... -
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miRDP2
Accurately and fast analyzing microRNAs transcriptome in plants
...We have tested miRDP2 to analyze miRNA transcriptomes in such plants with gradually increased genome size as Arabidopsis, rice, tomato, maize and wheat. Compared with miRDeep-P and several other computational tools, miRDP2 processed NGS data with superior speed. By incorporating newly updated plant miRNA annotation criteria, the accuracy of miRDP2 is also markedly improved. Our results demonstrate miRDP2 as a fast and accurate tool for analyzing the miRNA transcriptome in plants. Reference: https://doi.org/10.1093/bioinformatics/bty972 -
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Earth Enterprise
Google Earth Enterprise - Open Source
Earth Enterprise is the open source version of Google Earth Enterprise (GEE), a powerful geospatial application suite that enables organizations to build and host custom 3D globes and 2D maps using their own imagery and data. Unlike Google Maps or Google Earth, Earth Enterprise does not include Google’s proprietary imagery but instead provides the tools needed to manage and visualize private geospatial datasets. The system is composed of three main components: Fusion, which processes and integrates imagery, vector, and terrain data into unified map layers; Server, which hosts the resulting globes or maps via Apache or Tornado-based web servers; and Client, which includes the Google Earth Enterprise Client (EC) for 3D visualization and the Google Maps JavaScript API V3 for 2D viewing. ... -
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PINCIS
PINCIS.pl is a Perl bioinf. script to analyze PICS data
PINCIS.pl (PIcs N-/C-terminal Inferred Substrates perl script) is a small, command line tool to designate and analyze PICS (Schilling et al., Nat. Protocols, 2011) data to gain the prime and non-prime site specificity of proteases. Thus, the script filters given peptide lists for library peptides (generated by the digestion protease in the proteomics workflow rather then the protease of interest) and prints out lists of inferred N- and C-terminal cleavage window extensions which can be... -
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GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
...Basically, GenSeed-HMM performs three operations, repeatedly: - recruit reads by matching them to a seed - assemble the recruited reads (including previously assembled contigs) - generate new seeds (for the next round of progressive assembly) from the extremities of all generated contigs The first seed is provided by the user, and can be a piece of DNA or protein sequence, or an HMM profile, for increased sensitivity. This program depends on BLAST+ or hmmsearch and a number of third-party support tools (EMBOSS' transeq and splitter, bowtie, 454's sfffile and sffinfo). Which tools will be mandatory depends on the kind of seed and assembler used. Assemblers currently supported include CAP3, Newbler, SOAPdenovo, Velvet, and Abyss. -
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chklinks is a non-threaded Perl link checker. It helps finding broken links on your website. It does not raises many simultaneously connections for its job, run out of the resources and crash your system in a moment.
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Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.
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ApVSys is a general open-source wrapper designed for engineering Unix/Linux environment..It provides a way to use and manage simultaneously different versions of applications (engineering tools, compilers, debuggers simulators, ... ).
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TaxOnTree
A program for associating taxonomic information in a phylogenetic tree
...TaxOnTree turns its user into an expert on taxonomy. TaxOnTree also corrects for the absence of some taxa in NCBI taxonomy. Command line program is easy to set up and can be coupled to several bioinformatics tools, producing a colored tree in PDF format. TaxOnTree is available as a web tool in http://biodados.icb.ufmg.br/taxontree for low demanding jobs. -
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SDF or Structures Data File is a file format developed by MDL to handle a list of molecular structures with associated properties. The SDF toolkit provides small tools to read and parse SDFs, filter, and add/remove properties.
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htcontrol
controls high-temperature single-crystal XRD experiments using IPDSII
htcontrol is a software to control high-temperature single crystal XRD experiments on a STOE IPDS II or 2T diffractometer platform. A Manson SDP2210 power unit is needed as well as the ICP DAS I7019 data acquisition interface (amount of investment approx. 600 EUR). htcontrol is written in Perl and runs on a cygwin platform to be installed on the WinXP/10 host. Data collections are performed with Stoe's WinXpose (>=1.7.3) via the non-interactive XML interface.
