Search Results for "method"
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Showing 53 open source projects for "method"
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fwknop
Single Packet Authorization, Port Knocking
fwknop stands for the "FireWall KNock OPerator", and implements an authorization scheme called Single Packet Authorization (SPA). This method of authorization is based around a default-drop packet filter (fwknop supports iptables and firewalld on Linux, ipfw on FreeBSD and Mac OS X, and PF on OpenBSD) and libpcap. SPA is essentially next-generation port knocking (more on this below). The design decisions that guide the development of fwknop can be found in the blog post "Single Packet Authorization: The fwknop Approach". -
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HtmlDocument
A perl module to build simple html documents
...This does NOT cover ANY POSSIBLE html tags and is not a replacement for the usage of native html coding itself. The user still need to know about html and can add arbitrary html using the add_html() method. -
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C-squares
Concise spatial query and representation system (c-squares)
C-squares is an easily implemented method for storage, querying and display of spatial data locations, based on a hierarchical, grid-based representation of the Earth' surface. Source code for encoding, decoding, mapping, etc. is provided via this site. Additional support is available by contacting the system developer, Tony.Rees@marinespecies.org; see also the c-squares home page at http://www.cmar.csiro.au/csquares/ . -
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MMAP
Multi-core Method for Analysis Pipelines
For more information, please see home page. -
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Microarray assosiated motif analyzer
Cis-element prediction tool from microarray data
We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. ... -
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Safe Harbor Deidentification
Safe Harbor Deidentification for medical documents
Phalanx - Deidentify Safe Harbor Deidentification Mode of Phalanx is an abridged pipeline of NLP annotators culminating in NER annotators which write output of text offsets. It uses the Safe Harbor deidentification method. -
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WeBWorK is an web-based method for delivering individualized homework problems. It gives students instant feedback and allows instructors to track their progress in real time. Problems are written in a flexible and easy to use language. Current builds of this project are at https://github.com/openwebwork
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CABBaGe
Classification Algorithm Based on a Bayesian method for Genomics
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datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS experiment using a sliding window of a user-specified size, calculates overall parameters (I(0), Rg, Dmax and MW) and predicts the folding state (folded/unfolded) of the sample. ... -
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A thin, role-based, single image system for scalable cluster management. oneSIS is a simple, flexible method for managing one or more clusters from a single filesystem image. It is easy to deploy, and it simplifies the task of cluster administration.
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Placnet
Placnet project
...Please cite PLACNET as: Lanza VF, de Toro M, Garcillán-Barcia MP, Mora A, Blanco J, Coque TM, de la Cruz F: Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences. PLoS Genet 2014, 10:e1004766. -
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ISVASE
identification of sequence variant associated with splicing event
...However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data. Comparing with the existing software PVAAS, our method has several advantages such as stringent rule-depended filters and statistical filters in each step, detection sequence variants for known splicing events, identification sequence variants in two parts of splicing (junction) separately, detection junction shift events if providing known splicing annotation, evaluating splicing signal, comparing with known DNA mutation and/or RNA editing data, and short running time. -
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A machine learning-based method for somatic variant identification from low-pass next-generation sequencing.
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netool toolkit 4.6
MitM pentesting opensource toolkit
...Rootsector module allows you to automate some attacks over DNS_SPOOF + MitM (phishing - social engineering) using metasploit, apache2 and ettercap frameworks. Like the generation of payloads, shellcode, backdoors delivered using dns_spoof and MitM method to redirect a target to your phishing webpage. recent as introducted the scanner inurlbr (by cleiton) -
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SPA
SPA: a short peptide assembler for metagenomic data
...A nucleotide assembly-based strategy does not fare much better since metagenomic assemblies are typically very fragmented and also leave a large fraction of reads unassembled. We present a method for reconstructing complete protein sequences directly from NGS metagenomic data. Our framework is based on a novel Short Peptide Assembler (SPA) that assembles protein sequences from their constituent peptide fragments identified on short reads. We also present a new implementation of SPA based on suffix array (SFA-SPA) which runs significantly faster than SPA. ... -
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PRIMUS
Pedigree Reconstruction and Identification of a Maximum Unrelated Set
NEW: Download new version with Pedigree Reconstruction at primus.gs.washington.edu This versions is outdated and incomplete. Please visit the new website for the complete version of PRIMUS. We present a method adapted from graph theory that always identifies the maximum set of unrelated individuals in any dataset, and allows weighting parameters to be utilized in unrelated sample selection. PRIMUS reads in user-generated IBD estimates and outputs the maximum possible set of unrelated individuals, given a specified threshold of relatedness. ... -
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Dear all UPDATE Skalax using ActivePerl 5.16.3 UPDATE Ai Route method for move Config.txt and Timeouts.txt need to b fix manaully. route_step 8 for hi speed moveing or route_step 12 for INC agi moveing or route_step 15 for normal moveing Wiki : https://sourceforge.net/p/skalax/wiki/How%20to%20use%20EasyPlugin/ ai_talkAuto 3 ai_talkAuto_wait 3 ai_modifiedTalk_giveup 20 ai_route_npcTalk 3 Config.txt modifiedTalk 0 For the first user you have to setup perl 5.14.02 or perl 5.14.0.4 before and download fullsetup here https://sourceforge.net/projects/skalax/files/fullsetup/ Skalax is newbie Kore by Skalax Panama This project was developed from closed project name "tk". ...
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MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
...The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in SNP and genotype calling based on non-bisulfite treated reads. -
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bnns
Research tool for interactive training of artificial neural networks.
BNNS is a research tool for interactive training of artificial neural networks based on the Response Function Plots visualization method. It enables users to simulate, visualize and interact in the learning process of a Multi-Layer Perceptron on tasks which have a 2D character. Tasks like the famous two-spirals task or classification of satellite image data. -
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A pipeline to revise a genome sequence of a prokaryotic sample via an iterative backbone remapping and local assembly method.
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FastAlign.pl
FastAlign is a perl script which uses the heuristic method of tfasty
FastAlign.pl provides a more intuitive output to find exon-intron junctions. The query string is in amino acids and the hit string is in nucleotides. There are extra nucleotides at the end of the hit string (option -diff and by default = 10), that allow to verify if the intron start with common rules (5'-GTGCGA-... for group II intron and after an exonic T for group I intron). If you have Emboss, you can genarate a graphic with option -graph 1. Dependencies: - Perl - Bioperl - UNIX... -
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AHT (Ashiyane Hack Tools Ver) 1.1
Perl Hacking Tools (BackTrack)
...It is For BackTrack This Script Contains This tools : Local File Disclource (LFD) Checker Scanning the whole netmask and returning IP and MAC BackConnect Tools Proxy Checker Reverse IP Add a User With Admin Access (Windows) Add a User With r00t Access (Unix) Grab Cpanel Users Remote Port Scanning With NetCat SQL Injection Scanner MD5 Hash Cracker (Online) Admin Page Finder Make Uploader With Echo Method (Linux Servers) Service Scanning BruteForce Services With Medusa And Hydra (Backtrack) Test Lfi With php:// Bypass Method Cms Analyzer (Beta Version) Server Scanning With Nmap Remote Command Execution Console Fck Editor Scanner -
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SOAPsv
SOAPsv: is a program for detecting the structural variation
...Our approach accurately determines genotype and breakpoints relative to a reference genome based on de novo assembly of Illumina Genome Analyzer sequencing data. In this method, we examined only homozygous structural variations because detecting heterozygous structural variations requires assembly of haplotype sequences, which is not yet possible using existing assemblers. -
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TRF_Pathway
A Random Forest based Pathway association analysis tool
The TRF-pathway package implements the powerful two-stage random forest based pathway analysis. The manuscript discussing the method is currently under revision at PLoS One. -
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FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
