Search Results for "code alignment" - Page 3
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Showing 70 open source projects for "code alignment"
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MUSE
A library for Multilingual Unsupervised or Supervised word Embeddings
MUSE is a framework for learning multilingual word embeddings that live in a shared space, enabling bilingual lexicon induction, cross-lingual retrieval, and zero-shot transfer. It supports both supervised alignment with seed dictionaries and unsupervised alignment that starts without parallel data by using adversarial initialization followed by Procrustes refinement. The code can align pre-trained monolingual embeddings (such as fastText) across dozens of languages and provides standardized evaluation scripts and dictionaries. By mapping languages into a common vector space, MUSE makes it straightforward to build cross-lingual applications where resources are scarce for some languages. ... -
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arkwrt
A CLI tool for concepts defined in the ArchiMate® 2.1 specification
Arkwrt is a CLI (command-line interface) tool that provides a partial implementation of the ArchiMate® 2.1 Specification (ISBN: 978-94-018-0003-7). Arkwrt's creation was inspired by the The UNIX® philosophy that emphasizes building simple, short, clear, modular, and extensible code, that can be easily maintained and re-purposed by developers other than its creators. The UNIX® philosophy favours composability as opposed to monolithic design (see https://en.wikipedia.org/wiki/Unix_philosophy). Go was selected as the implementation language because of its alignment with the UNIX philosophy and for fun. If you notice a problem with using the program, please report it via Tickets. ... -
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adapter trimmer
We implement a very simple approach. Each read is searched for the jun
...If a match to either side of the junction is found then the entire 38bp juncton is clipped. This means the algorithm can tolerate an indel error in one of the sides of the junction, but not both. Optionally Smith-Waterman alignment can be turned on with -w which resolves this issue, although the code is less tested. eg. this will be caught: CTGTCTCT-TA-TACACATCTAGATGTGTATAAGAGACAG but not this: CTGTCTCT-TA-TACACATCTAGATGT-GTATAAGAGACAG -
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FOCUS
A model to identify organisms present in metagenomes in seconds
...The program was tested with simulated and real metagenomes, and the results show that our approach predicts the organisms in random communities. Availability and implementation: The code implemented in Python can be found here and a web-sever at http://edwards.sdsu.edu/FOCUS. Dependencies: Jellyfish, Numpy, and Scipy. Cite FOCUS Silva, G. G. Z., D. A. Cuevas, B. E. Dutilh, and R. A. Edwards, 2014: FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares. PeerJ, 2, e425,doi:10.7717/peerj.425. -
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Tabular
Vim script for text filtering and alignment
...Tabular is particularly helpful for Markdown tables, JSON-like configs, and code where lining up items improves scannability. By turning alignment into a repeatable operation, it reduces tedium and enforces consistent formatting across a project. -
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vim-easy-align
A Vim alignment plugin
...Because it’s fast and keyboard-centric, it’s ideal for refactoring code as well as tidying prose and documentation inside Vim. -
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The"Amip" GUI is intended to provide code examples of the methods proposed in: "Unsupervised image segmentation for microarray spots with irregular contours and inner holes" authors: Bogdan Belean, Monica Borda, Jörg Ackermann, Ina Koch and Ovidiu Balacescu Journal: BMC Bioinformatics, 2015, 16:412 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0842-3 PDE were used for grid alignment, whereas autocorrelation driven PDE and k-means clustering were used for spot segmentation. ...
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iMet-Q (intelligent Metabolomic Quantitation) is an automated tool with friendly user interfaces for quantifying metabolites in full-scan liquid chromatography-mass spectrometry (LC-MS) data. It has a complete quantitation procedure for noise removal, peak detection and peak alignment. In addition to accurate quantitation, iMet-Q provides the charge states and isotope ratios of detected compounds. It accepts input data in netCDF, mzXML, and mzML format and exports quantitation results in csv and txt format. The software source code is freely available under the license of GPL2.
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Java Wizard Development Framework
Reduced SWING coding. New UI components. Easy layout management.
About: 1) Projects helps Java - SWING developers to develop UI forms very faster. 2) API contains reusable Components & Layouts that developers can directly use in their projects. 3) Just include project JAR file in your existing project then import and use all features (refer JavaWizardDevelopmentDocumentation) * Don't worry about Java's complex layouts, just pass your components as parameters to our "MyLayout" class and we'll do it for you. * New & pre-aligned UI components like... -
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SimplyTheBlast
Blast query sequences on a set of fasta formatted genomes
SimplyTheBlast: a small perl tool to build genes presence/absence matrices over a set of Fasta formatted genomes. This code requires: Bio::SeqIO; Bio::Perl; Bio::Tools::Run::StandAloneBlast; Bio::Seq; Bio::Tools::Blast; Bio::DB::GenBank; Bio::DB::WebDBSeqI; and BLAST 2.2.28 (blastall and formatcmd) installed and reachable from your command line Usage: perl SimplyTheBlast-Align.pl <fasta formatted seeds file> <path to genomes folder> <Alignment length threshold in %> <Alignment identity threshold in %> OR Usage: perl SimplyTheBlast-Evalue.pl <fasta formatted seeds file> <path to genomes folder> <Evalue threshold> Genomes files names must end with *.faa Output files: TABULAR_FBH_OUTPUT.xls is an Excel readable file with the identifier of the best hits found TABULAR_FBH_OUTPUT.csv is a file with the number of the best hits found query_n* files are fasta formatted files with the sequences of the best hits found bugs /comments: marco.fondi@unifi.it -
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calc2booktab.latex
Script for OpenOffice/LibreOffice to convert tables to Latex-Code
UPDATE: The project was moved to github (https://github.com/schober-ch/calc2booktab). The soruceforge page won't get any bugfixes, please use the github repo if you want to try this macro. -------------------------------------------------------------------------- A Python extension for OpenOffice/LibreOffice to convert selected cells to LaTeX-Code. Its similar to Calc2Latex, but typographic formatting is more advanced (numeric columns, dcolumn-package, booktab-package) Script is... -
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Normalize.css
A modern alternative to CSS resets
normalize.css is a small CSS file that provides a consistent baseline of default styles across browsers without erasing useful browser opinions. Rather than a “hard reset” that zeroes everything, it preserves sensible defaults for elements while fixing inconsistencies and edge cases that vary between engines. The project documents why each rule exists, targeting real-world quirks such as form control alignment, typographic defaults, and HTML5 element rendering. It is deliberately minimal and... -
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LaTeX Table Creator
Simple Cross-platform LaTeX table creator with a GUI and console app.
...It does not supply WYSIWYG view. The GUI application allows the user to paste text into the application select formatting, generate the LaTeX output and copy the LaTeX code. The GUI is written using wxWidgets. The console application uses an input and output file and flags to specify formatting. -
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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A peak caller for ChIP-Seq experiments that robustly handles short reads with *multiple* possible mappings. Releases are hosted here, but development source code is available at https://github.com/jakebiesinger/AREM. A Google group has been set up to help with questions from the community and for announcements of new builds. http://groups.google.com/group/arem-announcements
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Image and video acquisition for scientific applications, particularly in behavioral biology and neuroscience
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Sequence studio main package provides classes and interfaces for various kinds of sequence alignment. Differently from regular expressions it computes similarity with two initially unknown strings. Project page provides code generating applet.
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Hermes 4
Hermes 4 FP8: hybrid reasoning Llama-3.1-405B model by Nous Research
Hermes 4 405B FP8 is a cutting-edge large language model developed by Nous Research, built on Llama-3.1-405B and optimized for frontier reasoning and alignment. It introduces a hybrid reasoning mode with explicit <think> segments, enabling the model to deliberate deeply when needed and switch to faster responses when desired. Post-training improvements include a vastly expanded corpus with ~60B tokens, boosting performance across math, code, STEM, logic, creativity, and structured outputs. ... -
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Llama-3.2-1B-Instruct
Instruction-tuned 1.2B LLM for multilingual text generation by Meta
Llama-3.2-1B-Instruct is Meta’s multilingual, instruction-tuned large language model with 1.24 billion parameters, optimized for dialogue, summarization, and retrieval tasks. It builds upon the Llama 3.1 architecture and incorporates fine-tuning techniques like SFT, DPO, and quantization-aware training for improved alignment, efficiency, and safety. The model supports eight primary languages (including English, Spanish, Hindi, and Thai) and was trained on a curated mix of publicly available...
