Search Results for "reference management"
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Showing 27 open source projects for "reference management"
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refbase - Web Reference Database
Online bibliographic manager for research groups. Zotero-compatible.
refbase is a web-based bibliographic manager which can import and export references in various formats (including BibTeX, Endnote, MODS XML, and OpenOffice). It can make formatted lists of citations and offers powerful searching, rich metadata, and RSS. -
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CERCA
CERCA – Citation Extraction & Reference Checking Assistant
CERCA is an open-source research tool that supports the verification of bibliographic references in scientific manuscripts. It extracts references from PDF files and checks their existence and consistency against authoritative metadata sources, producing explainable diagnostics, audit logs, and reproducible reports. It is intended for: - Researchers performing final manuscript checks - Reviewers assessing reference consistency - Editors supporting editorial quality control -... -
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SAGA - System for Automated Geoscientific Analyses - is a Geographic Information System (GIS) software with immense capabilities for geodata processing and analysis. SAGA is programmed in the object oriented C++ language and supports the implementation of new functions with a very effective Application Programming Interface (API). Functions are organised as modules in framework independent Module Libraries and can be accessed via SAGA’s Graphical User Interface (GUI) or various scripting...
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QUAST
Quality Assessment Tool for Genome Assemblies
QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. It is maintained by the Gurevich lab at HIPS (https://helmholtz-hips.de/en/hmsb). For the most up-to-date description, please visit http://quast.sf.net. Below are just some highlights. QUAST computes several well-known metrics, including contig accuracy, the number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and manual). A... -
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
...Since version 4, we provide functionalities for management of genomes and transcriptomes, including genome alignment and annotation of transposable elements. A complete list of functionalities is available in our wiki (https://sourceforge.net/p/ngsep/wiki/Home/). BEFORE DOWNLOADING: The green button directs to the jar for command line usage. See the wiki for the GUI and other options -
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TexGen is a geometric textile modelling software package to be used for obtaining engineering properties of woven textiles and textile composites. Citing TexGen We would be grateful if you could acknowledge use of TexGen where appropriate and suggest using one of the following references: L P Brown and A C Long. "Modelling the geometry of textile reinforcements for composites: TexGen", Chapter 8 in "Composite reinforcements for optimum performance (Second Edition)", ed. P Boisse,...
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HSRA
Hadoop spliced read aligner for RNA-seq data
HSRA is a MapReduce-based parallel tool for mapping reads from RNA sequencing (RNA-seq) experiments. RNA-seq analyses typically begin by mapping reads to a reference genome in order to determine the location from which the reads were originated, which is a very time-consuming step. This tool allows bioinformatics researchers to efficiently distribute their mapping tasks over the nodes of a cluster by combining a fast multithreaded spliced aligner (HISAT2) with Apache Hadoop, which is a... -
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SPANDx
Comparative analysis of haploid next-generation genome sequence data
...The outputs generated by SPANDx can be imported into PLINK for microbial genome-wide association study (mGWAS) analyses. SPANDx can utilise PBS, SGE or SLURM for resource management. SPANDx can also run directly on the command line if no resource manager is available. For the most up-to-date version of SPANDx, check us out on GitHub: https://github.com/dsarov/SPANDx -
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Taurus
A python based User Interface library.
The Taurus Project has *moved* to: https://github.com/taurus-org/taurus This SourceForge page is *outdated* and kept for historical reference only. Taurus is a python framework for control and data acquisition CLIs and GUIs in scientific/industrial environments. It supports multiple control systems or data sources: Tango, EPICS, ... New control system libraries and data sources can be integrated through plugins. -
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That project (RMOL) aims at giving developers concerned by the Revenue Management arena a library delivering a reference implementation for most of the published algorithms and methods. That library is intended to be used in simulated environment: it does not intend to be used in real world production systems.
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PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. PRADA currently supports 7 modules to process and identify... -
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Graphical Grammar Studio
An user friendly grammar tool for natural language processing tasks
Full documentation with tutorials is included in the download package. Graphical Grammar Studio is a tool for applying grammars which behave as words acceptors/consumers and annotators. GGS grammars can be used to find and annotate sequences of words which respect certain conditions, in a given input. Its purpose is for creating NLP tools like phrase chunkers, named entity finders, pronoun co-reference solvers etc. A grammar is represented by a state machine which can be visualized, edited... -
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Docear
An Academic Literature Suite
Docear (pronounced dog-ear) is what we call an “academic literature suite”. It integrates everything you need to search, organize and create academic literature in a single application: a digital library, reference manager, PDF and file manager, note taking and mind mapping. And the best: Docear works seemlessly with many existing tools like Mendeley, Microsoft Word, and Foxit Reader. Docear is free and open source, based on Freeplane, funded by the German Federal Ministry of Technology... -
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Bika Open Source LIMS
Web based Open Source laboratory information management system (LIMS)
Modern Open Source LIMS (Laboratory Information Management System) · Professionally supported by experts The Bika code was migrated to https://github.com/bikalims Getting Started: https://github.com/bikalims/bika.lims/blob/main/README.md Modern Bika releases are built on the Senaite LIMS core, the LIMS that originated as a Bika fork. It is therefore as new and modern as Senaite, frequently upgraded and has many very useful add-ons. Bika expands on Senaite's lean design by adding... -
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libmx
A framework for dealing with lambda calculus expressions.
...Among other features it provides o a template instantiation machine for evaluating the value of an lambda calculus expression, o a template instantiation machine for evaluating the Hindley-Milner type (http://en.wikipedia.org/wiki/Hindley-Milner) of an lambda calculus expression, and o reference counter based memory management for lambda calculus expressions and types. "libmx" is written in C (C99). -
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CAPLET
GDS visualization and parallelized capacitance extraction
Project CAPLET is a capacitance extraction toolkit that extract capacitance at field-solver accuracy. CAPLET can directly handle GDS2 layout files into capacitance matrices in both GUI and command line interfaces. The internal extraction algorithm is specialized for VLSI interconnect structures but not exclusively, as long as the structure is of Manhattan geometry and embedded in a uniform dielectric material. -
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mathrefplugin
A plugin for JabRef
A plugin for JabRef. The plugin queries Zentralblatt MATH reference entries using the BibTeX format. -
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GeoPMS is a project based full paper management system to archive, search and manage scientific papers. GeoPMS has full text search, search by author, search by title and citation import functionality direct from the PDF header, PDF text or RIS. Reference list design can be selected for each project.
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JFinisher
JFinisher is software for alignment, editing and manipulation DNA seqs
JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and ability to export results in the standard formats of the area. -
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PHPXref is a developers tool, written in Perl, that will cross reference and extract inline documentation from a collection of PHP scripts. It generates simple HTML output suitable for browsing offline.
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Ruby Research Wiki (RRiki) can be used to keep notes and organize references for research. It uses a browser interface, an intuitive plain text formatting language (markdown), and facilities to cross-reference and hierarchically organize notes
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Connotea is an online reference management system. It allows users to store and organise their links and scholarly references online, and can automatically import bibliographic data from online archives. This project hosts the source code for Connotea.
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Quick reference for switching between mathematical computation environments for computer algebra, numeric processing and data visualisation. Examples are Matlab, IDL, SPlus, and their open-source counterparts Octave, Scilab, Python+NumPy and R.
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Yabman is a tool for managing bibliographic references. Its key features are a quality user interface, a carefully designed data model, and sophisticated three-state hierarchical reference labeling. It is currently usable but in a pre-alpha stage.
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Application Wireframe XML and reference software/stylesheets. This project aims to create a xml schema for application wireframes used during requirements gathering phase of development. The goal is a methodology and programming language agnostic format.
