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Showing 47 open source projects for "paper"
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multinotes
Text architecture for music theory.
The text structures of notes and publications in music theory and musical analysis bring challenging requirements: how to include music notation excerpts, graphics, and even combinations thereof, into the typeset flow of paragraphs and into the work-flow, and how to integrate navigable references to these and to single domain entities into running text. Furthermore, dynamic interactive documents can be useful for presenting complicated interdependencies to the reader more clearly, far beyond conventional paper publication. The mulitNotes text architecture and processing pipeline is based on d2d and standard technologies (XSLT, ECMAScript. LilyPond, PostScript, etc.) and addresses these issues. An overview about the software architecture and its operation is given in: Journal of the Text Encoding Initiative, Open Issue 18/2024: "Using d2d for Writing XML --- The multiNotes Text Architecture for Musical Analysis" https://doi.org/10.4000/132ex -
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Ket
An algebra editor
A text editor for maths. Simple algebra should be faster and more intuitive to perform on a computer than on paper and should look like maths. Write small fragments in plain text; perform simple click-and-drag algebra with the mouse; and explore more involved algebra through keyboard shortcuts. When done, save as plain text files or export to LaTeX and HTML. -
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StatisticsTables
This is a Java APP for Probability and Statistics Tables
If you have Windows or a MAC , you can setup and run Statistics Tables with very little effort. You can use jdistabs in place of paper Probability Tables to get electronic probabilities. You can also download the Java code used to create this APP. There are 2 zips. One is for a working windows APP, and the other with complete code and file structure. I used Eclipse to develop the APP. Click the link you want to download to get the Statistics Tables Windows.exe or OS X zipped files. ... -
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COHCAP
City of Hope CpG Island Analysis Pipeline
...Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub. 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download -
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The main purpose of CombiTagger is to read files generated by individual PoS taggers and use them to develop and evaluate combined taggers according to a given combination algorithm. http://aaai.org/ocs/index.php/FLAIRS/2009/paper/download/67/296
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spectralHMM
A spectral method for inferring selection from time series data
***WARNING*** This software was migrated to: https://github.com/popgenmethods/spectralHMM Support and updates will only be available at this new address. This software implements the algorithms described in the following paper: Steinrücken, M., Bhaskar, A. and Song, Y.S. A novel spectral method for inferring general diploid selection from time series genetic data. Annals of Applied Statistics, Vol. 8, No. 4 (2014) 2203-2222 -
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Maps coloring
Four color theorem application
Search for a pencil and paper proof of the four color problem. See http://4coloring.wordpress.com for info. Please let me know what you think about this application. Also visit the youtube channel: http://www.youtube.com/user/mariostefanutti/videos -
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YoMo
You Only Meter Once - The open hardware smart metering system
...On top of the software runs a apache webserver that provides all estimated data on our yomo project homepage. The system does not need any maintenance and works out of the box after the devices were integrated into the households Wi-Fi network. Link to the scientific paper: http://link.springer.com/article/10.1007%2Fs00450-014-0290-8#/page-1 -
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G4LTL-ST
Generating PLC programs from formal specifications
G4LTL-ST is a standalone tool and a Java library for automatically generating industrial control software (supporting IEC-61131-3 Structure Text) from LTL or extended logic specifications. See Tutorial.txt inside the package for step-by-step instructions. For technical demails, see CAV'14 paper "G4LTL-ST: Automatic Generation of PLC Programs". The old version (G4LTL; under BSD license) is available under file\arxiv. -
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Econball
Equation of stock trading simplified to game of moving resizing balls
...Those who change to the majority side lose, and those who change to the minority side win, since it is scaled to the average. Its the same math as Matching Pennies and Odds And Evens game which are Rock Paper Scissors with 2 choices instead of 3 (buy vs sell). You see this in the size of balls changing depending where they move. Think of it as a 2d seesaw surface that never tilts because the masses of balls are adjusted to always balance. This is the early start of a game based on that econ theory. Econ is boring in number and symbol form, but as a realtime game its more like dancing. -
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Jafaran
Fast and more random implementations of java.util.Random.
...The names of implementations contain "Conc" (for concurrent) if they are thread-safe and non-blocking, or "Seq" (for sequential) if they are not thread-safe. Also provides an implementation of Ziggurat algorithm (based on J. A. Doornik paper, 2005), used by nextGaussian() methods of the provided implementations. Requires Java 5 or later. Also available on github since 2015/12/13: https://github.com/jeffhain/jafaran Principal classes: - Implementations using Mersenne-Twister algorithm (good pseudo-randomness): MTSyncRNG MTSeqRNG - Implementations using Marsaglia Xor-Shift (fast): MXSIntSeqRNG (32 bits) MXSLongSeqRNG (64 bits) (nextLong() faster, larger period) - Ziggurat: Random-based implementation of Ziggurat algorithm. -
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Lab Processes
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Lab Processes. We want to hear your feedback! Request new Lab Processes feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/lp Lab Processes is a comprehensive and straightforward application specially designed for biologists and chemists who need to conduct a wide variety of tests and experiments on animals. Lab Processes requires minimal computing skills. Genetic and physiological data can be entered either... -
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MattsMathTools
MathTools is an aid in preparing printed math tests.
Matt's MathTools is a Java application designed as an aid in preparing printed math tests. It is easily embedded in other Java applications or it can be used alone as a single-user desktop app. It includes a scripting environment, numerous demonstration classes and several general utilities. A scripting tutorial is also available. -
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Virmid
Virtual Microdissection for SNP calling
NEWS: 11-07-2013 A new version Virmid 1.1.0 has been uploaded. 08-29-2013 Virmid paper is now published in Genome Biology. Kim S et al, "Virmid: accurate detection of somatic mutations with sample impurity inference", Genome Biology 2013, 14:R90 http://genomebiology.com/2013/14/8/R90/abstract Virmid (Virtual Microdissection for SNP calling) is a Java based variant caller designed for disease-control matched samples. -
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SuRankCo
Supervised Ranking of Contigs in de novo Assemblies
...For more details about SuRankCo and its functioning, please see "SuRankCo: Supervised Ranking of Contigs in de novo Assemblies" Mathias Kuhring, Piotr Wojtek Dabrowski, Andreas Nitsche and Bernhard Y. Renard (http://www.biomedcentral.com/1471-2105/16/240/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo. Update Jun2015: * Minor changes to enable BAM support. Update Feb2014: * Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL). NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet. -
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LiDSiM
LImits of Detection SImulation for Microbes
...For more details about LiDSiM and its functioning, please see "Estimating the Computational Limits of Detection of Microbial Non-Model Organisms" Mathias Kuhring and Bernhard Y. Renard (http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400598/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using LiDSiM. -
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DCTFinder
Extract title and creation time from web page.
...DCTFinder combines heuristic title detection, supervised learning with Conditional Random Fields (CRFs) for document date extraction, and rule-based creation time recognition. DCTFinder is released under CeCILL free software license agreement. The system is described in the following paper (see 'Files' section): Xavier Tannier. "Extracting News Web Page Creation Time with DCTFinder". Proceedings of the 9th Language Resources and Evaluation Conference. Reykjavik, Iceland. -
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TUIT
Taxonomic Unit Identification Tool
...A new field has been added to the properties.xml, please make sure to update it to contain <OutputFormat format="tuit"/> or <OutputFormat format="rdp"/> in the <BLASTNParameters> section. Read our paper in Biotechniques: http://www.ncbi.nlm.nih.gov/pubmed/24502797 Taxonomic Unit Identification Tool (TUIT) is a free open source platform-independent software, designed specifically to facilitate taxonomic annotation of nucleotide sequences via BLAST homology search against the NCBI databases. TUIT is immediately applicable for both to 16S microboime studies as well as for taxonomic classification of the nucleotide reads. ... -
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BioAnnote
Annotator Desktop application is able to annotate biomedical texts by
...In addition, users can retrieve more detailed information for each recognized entity (making use of an integrated web browser), including related topics, external links, related bibliography and paper abstracts. -
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This is the program and data to accompany both the thesis and paper under the name A MINE ALTERNATIVE TO D-OPTIMAL DESIGNS FOR THE LINEAR MODEL This contains the program and summary of the data used for the paper.
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cmotif
A method for mining conditional phosphorylation motifs
...Although several algorithms have been proposed to uncover phosphorylation motifs, the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. In this paper, we propose an algorithm called C-Motif for a non-redundant identification of significant phosphorylation motifs. In tests with real data including both non-kinase-specific and kinase-specific phosphorylation data, the C-Motif algorithm successfully reports a relatively complete set of of conditional phosphorylation motifs efficiently. -
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BioLemmatizer
Lemmatization tool for morphological analysis of biomedical literature
...README: https://sourceforge.net/projects/biolemmatizer/files/ The BioLemmatizer 1.2 release adds an optional functionality to normalize British English spellings into American English spellings and then retrieve corresponding lemmas. If you use the BioLemmatizer to support academic research, please cite the following paper: Haibin Liu, Tom Christiansen, William A Baumgartner Jr, and Karin Verspoor BioLemmatizer: a lemmatization tool for morphological processing of biomedical text Journal of Biomedical Semantics 2012, 3:3. -
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AMESProject
A "simple but not too simple" laboratory for wholesale power markets.
The wholesale power market design proposed by the U.S. Federal Energy Regulatory Commission (FERC) in an April 2003 white paper [FERC 2003] encompasses the following core features: 1. Central management by an independent market operator. 2. A two-settlement system consisting of a day-ahead market supported by a parallel real-time market to ensure continual balancing of supply and demand for power. 3. Management of grid congestion by means of locational marginal pricing (LMP), i.e., the pricing of power by the location and timing of its injection into, or withdrawal from, the transmission grid. 4. market power oversight and mitigation. -
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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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...Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the following paper: Ehsan Emadzadeh, Azadeh Nikfarjam, and Graciela Gonzalez. 2011. Double Layered Learning for Biological Event Extraction from Text. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistic
