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Showing 22 open source projects for "so"
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Prokka
Rapid prokaryotic genome annotation
...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. Because it standardizes names, locus tags, and qualifiers, Prokka is often used as a baseline for comparative microbial genomics, pangenome studies, and functional profiling. ... -
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Th3inspector
Best Tool For Information Gathering
...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 from one script. The project provides simple install wrappers for Linux, Android/Termux and even instructions for Windows (Perl + CPAN modules), and includes helper scripts to update or install dependencies automatically. The repository is actively packaged as versioned releases in the README (current noted version 1.9) and is distributed under an MIT license. -
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New Debian package available 30th April 2021, lots of bugs corrected. Currently code a little ragged as of June 2026 watch this space for new package. Simple system for displaying civic features, opportunities and problems on a rasterised map. Currently to map 'informal gardening' and foraging for useful items on the street. Simple to set up and use. Can be parametrised for specific usage. Installation description, to be expanded in: https://sourceforge.net/p/datamap/wiki/Installation/
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In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing events. In so doing, it is feasible to compare two samples and identify genes with most significant difference in exon(splicing)-level.
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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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mers
Portable software and data related to Mersenne numbers
...Useful to automate certain tasks related to GIMPS (www.mersenne.org) for computers that cannot run the GIMPS software for whatever reason. Much of the code has been in use since 1990 or so by a few people. The project web site at https://mers.sourceforge.io/mersenne.html has data about Mersenne numbers from many people generated by this and other software, notably from the GIMPS project. -
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The Simplest Manual Counter
Manual counter with the keyboard or the mouse on images
...After associating a key to each item, or a predefined graphical symbol for images, pressing the key or clicking on the image increments its associated counter, and displays (for the images) the symbol at the mouse's pointer location. Such a project is so simple a child could use it! -
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SmGen
Verilog Finite State Machine (FSM) Code Generator
...The input is behavioral Verilog with clock boundaries specifically set by the designer. SmGen unrolls this behavioral code and generates an FSM from it in synthesizable Verilog. Clock boundaries are explicitly provided by the designer so there is good control on the expected timing -
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BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
...In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj -
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Perl OBD-II Logger
A Perl program for logging OBD-II PID data
...By default, the output log file contains time-stamped PID values in a simple Comma Separated Values (CSV) format that can be readily imported into popular data analysis or spreadsheet applications. (Output to an SQLite3 database file is also available). It is written in Perl, so it runs in any computing environment with a working Perl interpreter. The program supports scantools that are based on the ELM Electronics ELM327 or OBD Solutions STN1110 programmed microcontrollers. It has been tested with scantools using legacy RS-232 serial, serial over USB, and Bluetooth hardware interfaces. Perl OBD-II Logger even runs on the popular Raspberry Pi computer! -
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iMir
Integrated pipeline for HT miRNA-Seq data analysis
...To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular pipeline, called iMir, integrating multiple open source modules and resource in an automated workflow, devising different statistical approaches to analyze data rigorously. iMir comprises also a Graphical User Interface (GUI), so that the pipeline is particularly suited for biologist and early stage bioinformaticians and produces both graphics and text outputs. -
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Digital Expression on the Web
DEW is a platform that allows users to explore RNA-Seq data
...A web-based Graphical User Interface is included. The analysis proceeds as such: gapped alignments are performed and corrected for length, PCR and fragment bias so that a Fragment Per (effective) Kilobase per Million of reads (FPKM) is estimated as well as the simpler Reads Per Kb per Million of reads (RPKM). When provided with multiple isoforms and in the ‘contextual’ mode, corrections include a expectation maximization algorithm estimates effective expression profiles and a corrected alignment is produced. ... -
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modDFS
Find whether a KEGG module is complete in a proteome
...For cyclic modules, completion is defined as having all the module reaction steps present. Again, lenient completion cases are reported. Also, all absent reactions are reported so that a manual inspection of completion can be done for modules that are parially cyclic. -
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...It is not intended for "normal" end-users, but for network administrators and operations groups. You will need to install Apache (or any other web server) with PHP, configuring apache in the proper way for directories permissions and so on. Find more pictures and info in the docs.
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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ParaSim
Parallelized calculation of molecular similarities
...ParaSim calculates chemical similarities based on binary structural fingerprints. It does not compute fingerprints by itself but relies on third party software to do so. Basically, all types of structural fingerprints which can be stored in an array of bits (a bitset) can be used by ParaSim. See the Wiki (https://sourceforge.net/p/parasim/wiki/Documentation/) for detailed documentation. FEEDBACK HIGHLY APPRECIATED! -
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hrefinder
Detection of homologous recombination events from SNP data
...It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of SNPs differs from the ancestral allele, it may be better explained as a mutation or sequencing error. But if a series of SNP alleles differ from the ancestral pattern, then it may be more likely that an HRE has occurred, particularly if the allele pattern matches that from another part of the tree better than that of the ancestral node. -
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A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper
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An experimental CEP (Complex Event Processing) engine. It implements the event stream processing as a library embeddable in C++ and Perl. Since then it has been renamed to Triceps, so please look at the new location https://sourceforge.net/projects/t
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This is a unix distribution I made so that I can develop from anywhere--a virtual desk if you will. Some of my friends and colleagues have found it useful, and an easily accessible place to put the operating system up is on the internet.
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Geographic tag manipulator - a simple XSLT-based tool to add, remove, or change tags of OpenStreetMap objects.
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MyGenBank is a set of OpenSource software for managing a local copy of GenBank (www.ncbi.nih.gov/Genbank). It is implemented using Perl, MySQL, and Linux so that you can manage a complete or partial copy of GenBank on a computer as small as a laptop.
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The GPS Ride Plot project is software to convert a downloaded GPS track and generate a map image in PNG format. This has been used primarily to plot bicycle rides. It can also plot almost any GPS track and has done so for cars, trolleys or jet airliners.
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