Scientific/Engineering Software

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Scientific/Engineering Software

  • Want to improve your MSP’s revenue? Price your services right. Want to improve your MSP’s revenue? Price your services right. Icon
    Want to improve your MSP’s revenue? Price your services right. Icon

    Get the ebook, The Managed Services Pricing Guide 2.0 to get industry best practices on pricing managed services.

    You choose software for your IT business so it makes you money. The margins must be good enough to justify the cost. SolarWinds RMM was priced to give you the margins you need to earn a healthy amount of monthly recurring revenue. Download our all-new Managed Services Pricing Guide 2.0 to find what revenue to expect for your services, including light monitoring, web protection, patching management, backup and more.
  • Take Our Survey. We Plant a Tree. Take Our Survey. We Plant a Tree. Icon
    Take Our Survey. We Plant a Tree. Icon

    In honor of Earth Day, HPCC Systems is committed to planting 10,000 new trees across our national forests.

    HPCC Systems is dedicated to the environment and is giving you the opportunity to take action and be a small part of a big impact. In partnership with the National Forest Foundation, HPCC Systems is growing and promoting awareness of environmental sustainability with their 10K Trees Challenge. The best time to plan a tree was 20 years ago. The second best time is now! Take our survey and take part in helping the environment.
  • Open Nautical Charts Icon

    Open Nautical Charts

    Open Nautical Charts offers free seacharts for everybody. This charts are usable (offline) with several ship-plotters and Navigation-equipement on board. kap, Png, Jpr, png-cal, For user with Open CPN or SeaClear and other.

  • Bridge Designer and Contest Icon

    Bridge Designer and Contest

    A national virtual bridge engineering contest for kids of all ages.

    **Unfortunately, the Bridge Contest is no longer operational. We hope the code base will be of use to others with similar projects in mind.** 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. The new Rails back end is a RubyMine project. Thanks to JetBrains for this mega development environment!

    Downloads: 1,460 This Week Last Update: See Project
  • vcftools Icon

    vcftools

    A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/

  • NCO netCDF Operators

    Command-line operators for netCDF and HDF files

    The netCDF Operators, or NCO, are a suite of file operators which facilitate manipulation and analysis of self-describing data stored in the (freely available) netCDF and HDF formats. Volunteers welcome! See homepage for details and download links.

  • StarkOX Icon

    StarkOX

    Open Source Robot Operating System

    StarkOX, the first universal Open Source AI Robot Operating System. It provides easy to use hardware abstraction and commonly-used functionality. Furthermore, strong cognitive functions, voice and pattern detection together with a new powerful scripting language provide possibilities to create and share abstract behavior patterns.

    Downloads: 198 This Week Last Update: See Project
  • Pyramid - The Complete Self-Service Analytics Platform Pyramid - The Complete Self-Service Analytics Platform Icon
    Pyramid - The Complete Self-Service Analytics Platform Icon

    Easily combine data from multiple sources to build dashboards and reports with our scalable solution built for mid-size to enterprise companies.

    Pyramid combines analytic tools often found in separate applications. It features a graphically based ETL to model data and incorporate machine learning algorithms, intuitive data discovery tools that produce simple and advanced visualizations, a presentation builder for creating analytic applications and presentations, and an enterprise-grade report builder—all in a single, integrated platform that can be accessed from any browser or device.
  • PRINSEQ Icon

    PRINSEQ

    A bioinformatics tool to PRe-process and show INformation of SEQuence data. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.

    Downloads: 120 This Week Last Update: See Project
  • Automalator

    State Dependency deconstructor and mapper for C source code.

    Flowcharts not telling you what you want to know about some C source code? Try a State Dependency map! Every C source file is an implemention of a state machine. Implicit in the definition of a state machine is a network of dependencies between the states. The Automalator * deconstructs the C code into the core state machine * collates the transactions into the dependency net * generates a diagram-format file with the states and dependencies as the nodes and edges. Pre-requisites * Perl - tested with versions 5.12.3, 5.14.2 and 5.20.2, Windows, Linux and MAC * Get the Automalator by downloading the zip, or checking out or exporting the SVN trunk * copy the source code of interest into "project.c" * windows - double-click "src2map.bat" * linux & MAC - navigate the command line to the "project" folder, then run "src2map.sh" * open "project.gml" file with diagramming software.

    Downloads: 74 This Week Last Update: See Project
  • Seqping

    Gene Prediction Pipeline for Plant Genomes

    Gene Prediction Pipeline for Plant Genomes using Self-Training Gene Models and Transcriptomic Data

    Downloads: 52 This Week Last Update: See Project
  • miRDeep-P Icon

    miRDeep-P

    miRDeep-P,miRDP for short, is a computational tool for analyzing the microRNA (miRNA) transcriptome in plants.

  • BreakDancer

    BreakDancer-0.0.1 is a Perl package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

  • One Backup & Disaster Recovery Solution for Any Need One Backup & Disaster Recovery Solution for Any Need Icon
    One Backup & Disaster Recovery Solution for Any Need Icon

    SherWeb Online Backup Is Your Easy Solution for Cloud & Local Backups. The App Is Free, Pay Only for the Cloud Data Storage.

    With the diversity of IT solutions used, managing backup and disaster recovery can turn very complex for a business. SherWeb Online Backup simplifies everything. You back up servers, desktops, virtual machines and smart devices, plus popular applications and Office 365 data – all from a single web-based console. Active Protection, the embedded anti-ransomware feature, adds a security layer while the Cloud-to-Cloud feature saves network bandwidth.
  • AdamaJava

    Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/

    Downloads: 34 This Week Last Update: See Project
  • GEM library

    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

    Downloads: 31 This Week Last Update: See Project
  • BIGSdb

    Software for storing and analysing bacterial sequence data

    The Bacterial Isolate Genome Sequence Database (BIGSdb) is a scalable, web-accessible database system designed to store and analyse linked phenotypic and genotypic information in a computationally efficient manner. Sequence data can range from single sequence reads to multiple contigs generated by whole genome sequencing technologies. The system incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into schemes for isolate characterisation or for evolutionary or functional analyses. See Jolley and Maiden 2010, BMC Bioinformatics 11:595 (http://www.biomedcentral.com/1471-2105/11/595). You can report bugs or make enhancement requests using the issues tracker at https://github.com/kjolley/BIGSdb. The source code is also mirrored there.

  • basecv

    BCV is DNA base caller with vocabulary

    The Base Calling with Vocabulary (BCV) software package is intended for analysis of direct (population) sequencing chromatograms using known vocabulary sequences similar to the target DNA. The current version of BCV can only process chromatogram files obtained on Applied Biosystems capillary sequencing machines (ABIF file format).

    Downloads: 20 This Week Last Update: See Project
  • SVDetect Icon

    SVDetect

    A tool to identify genomic structural variations from paired-end and mate-pair sequencing data

  • ParseCNV

    ParseCNV CNV call association software takes CNV calls as input and creates SNP based statistics for CNV occurrence in population study cases and controls then calls CNVRs based on neighboring SNPs of similar significance.

  • DeconSeq Icon

    DeconSeq

    The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. More at http://deconseq.sourceforge.net

  • PhaseTank

    genome-wide computational identification of phasiRNAs

    Phase siRNAs (phasiRNAs) are a class of small RNAs, which triggered by miRNA-targeted cleavage and followed by DCL4-mediated production of small RNAs phased in 21-nt increments. Here, we introduce PhaseTank to systematically characterize 'miRNA → mRNA → tasiRNA → target genes' regulatory casacades in plants. With one command analysis, PhaseTank is an easy-to-use software for users.

    Downloads: 11 This Week Last Update: See Project
  • Meraculous-2D

    Eukaryotic Genome Assembler

    !!! NEW !!! 1/2017 - We now have a version optimized for running Human assemblies on AWS: https://sourceforge.net/projects/meraculous20/files/Meraculous-v2.0.5.2-smp_patch1-2-gcac7312.tar.gz/download ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Fast and memory-efficient k-mer counts - Efficient deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. The assembly is driven by a robust pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a Grid Engine-type cluster or a standalone multi-core server. Manuscripts in submission: https://arxiv.org/abs/1703.09852 https://arxiv.org/abs/1608.01031

    Downloads: 10 This Week Last Update: See Project
  • LMAP Icon

    LMAP

    Lightweight Multigene Analyses in PAML

    Maldonado E, Almeida D, Escalona T, Khan I, Vasconcelos V and Antunes A (2016) LMAP: Lightweight Multigene Analyses in PAML. BMC Bioinformatics, 17:354. doi: 10.1186/s12859-016-1204-5

    Downloads: 9 This Week Last Update: See Project
  • Perstem Icon

    Perstem

    Perstem is a Persian (Farsi) stemmer, morphological analyzer, transliterator, and partial part-of-speech tagger. Inflexional morphemes are separated or removed from their stems. Perstem can also tokenize and transliterate between various character set encodings and romanizations.

  • MicroGP Icon

    MicroGP

    A multi-purpose extensible self-adaptive evolutionary algorithm

    MicroGP (uGP) is a versatile optimizer able to outperform both human experts and conventional heuristics in finding the optimal solution of hard problems. It is an evolutionary algorithm since it mimics some principles of the Neo-Darwinian paradigm.

  • GenSeed-HMM Icon

    GenSeed-HMM

    Progressive assembly tool using DNA, protein or profile HMMs as seeds.

    GenSeed-HMM is a program for seed-driven progressive DNA assembly. It differs from the previously published GenSeed in many aspects, but more pointedly by being able to use an HMM profile as seed. 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.

    Downloads: 5 This Week Last Update: See Project
  • LOCUST

    Custom Sequence Locus Typer

    A Custom Sequence Locus Typer for Classifying Microbial Genotypic and Phenotypic Attributes. Publication: Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G. LOCUST: A Custom Sequence Locus Typer for Classifying Microbial Isolates. Bioinformatics (Oxford, England). 2017 Jan 27; https://www.ncbi.nlm.nih.gov/pubmed/28130240

    Downloads: 5 This Week Last Update: See Project
  • facile

    A command-line biochemical network compiler for systems biology.

    Downloads: 5 This Week Last Update: See Project

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