Search Results for "patterns"
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Showing 21 open source projects for "patterns"
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AlphaGenome
Programmatic access to the AlphaGenome model
...This repository contains client-side code, examples, and documentation to help you use the AlphaGenome API. AlphaGenome offers multimodal predictions, encompassing diverse functional outputs such as gene expression, splicing patterns, chromatin features, and contact maps. The model analyzes DNA sequences of up to 1 million base pairs in length and can deliver predictions at single-base-pair resolution for most outputs. AlphaGenome achieves state-of-the-art performance across a range of genomic prediction benchmarks, including numerous diverse variant effect prediction tasks. -
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Seamly2D
Free and open source pattern design software
Seamly2D enables the design, reuse, and remix of digital sewing patterns for creating bespoke-fit, specialty-sized, and ready-to-wear-sized clothing. Users have the right to utilize, sell, share, and distribute their patterns in any way they choose. * Downloads: https://seamly.io * Support: https://forum.seamly.io * Code: https://github.com/fashionfreedom/seamly2d * License: GPLv3+ -
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Croizat
A software package for quantitative analysis in Panbiogeography
Croizat is a free, user-friendly, cross-platform desktop software package which biologists can use to integrate and analyze spatial data on species or other taxa and to explore geographical patterns in diversity under a panbiogeographic and graph-theoretic approach. -
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Fosite - advection problem solver
numerical simulation code for solving transport equations in 1D/2D/3D
...In addition to the pure advection code several source terms have been implemented including viscous diffusion and gravitational acceleration. Fosite is written with object-oriented patterns in Fortran 2003 and follows the Structure of Arrays (SoA) layout, operating on generic field datatypes. This allows for high performance on modern architectures (SIMD). It is parallelized and vectorized. The software is thereby optimized for the NEC SX-Aurora TSUBASA Vector Engine . -
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NuPIC
Numenta platform for intelligent computing
...HTM is a detailed computational theory of the neocortex. At the core of HTM are time-based continuous learning algorithms that store and recall spatial and temporal patterns. NuPIC is suited to a variety of problems, particularly anomaly detection and prediction of streaming data sources. For more information, see numenta.org or the NuPIC Forum. If you want to build the dependent nupic.bindings from source, you should build and install from nupic.core prior to installing nupic (since a PyPI release will be installed if nupic.bindings isn't yet installed). ... -
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HyLiTE
Hybrid Lineage Transcriptome Explorer
...Allopolyploidy describes the formation of a new hybrid organism from the union of two or more different parents. Allopolyploid species carry multiple copies of each gene (homeologs), which often exhibit unusual expression patterns. Homeolog expression levels can technically be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to one homeolog over another is extremely challenging, particularly on a whole-genome scale. HyLiTE automates this process, and allows gene expression patterns to be explored even in very complex allopolyploid species. -
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Gene-Environment iNteraction Simulator 2
A tool able to simulate gene-environment and gene-gene interactions.
Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to be simulated or on number of non-predisposing genetic/environmental factors to be considered. The GENS2 tool is able to simulate gene-environment and gene-gene interactions. To make the Simulator more intuitive, the input parameters are expressed as standard epidemiological quantities. ... -
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ExSTraCS
Extended Supervised Tracking and Classifying System
This advanced machine learning algorithm is a Michigan-style learning classifier system (LCS) developed to specialize in classification, prediction, data mining, and knowledge discovery tasks. Michigan-style LCS algorithms constitute a unique class of algorithms that distribute learned patterns over a collaborative population of of individually interpretable IF:THEN rules, allowing them to flexibly and effectively describe complex and diverse problem spaces. ExSTraCS was primarily developed to address problems in epidemiological data mining to identify complex patterns relating predictive attributes in noisy datasets to disease phenotypes of interest. ... -
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mwetoolkit
THIS PROJECT MIGRATED TO https://gitlab.com/mwetoolkit/mwetoolkit3/
THIS PROJECT MIGRATED TO https://gitlab.com/mwetoolkit/mwetoolkit3/ The Multiword Expressions toolkit aids in the automatic identification and extraction of multiword units in running text. These include idioms (kick the bucket), noun compounds (cable car), phrasal verbs (take off, give up), etc. Even though it focuses on multiword expresisons, the framework is quite complete and can also be useful in any corpus-based study in computational linguistics. The mwetoolkit can be... -
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This project provides a Fortran90 library and a python module for singular spectrum analyses such as PCA/EOF or MSSA. It is intended for people interested, for example, in analysing climate or financial variability.
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PolyCTLDesigner
Python scripts for designing polyepitope T-cell immunogens
Given the peptides (T-cell epitopes) PolyCTLDesigner selects flanking sequences to optimize TAP-binding and joins resulting oligopeptides into a polyepitope in a way providing efficient liberation of potential epitopes by proteasomal and/or immunoproteasomal processing and minimizing the number of junctional epitopes. For constructing polyepitopes PolyCTLDesigner utilizes known amino acid patterns of proteasome cleavage and TAP-binding specificity. PolyCTLDesigner is also able to choose antigenic peptides covering selected HLA repertoire with desired redundancy rate. Given the antigen sequences PolyCTLDesigner is also able to select T-helper epitopes. For predicting T-cell epitopes it uses TEpredict. -
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Application to create 'electronic fluorescent pictographic' representations of gene expression patterns. Created at the Provart lab of the department of Cell & Systems Biology, University of Toronto.
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Ablator
A tool for automating laser ablations for neuroscience
Ablator is a suite of software that automates the microscopic detection of cell targets and also directs a 2-photon microscope to lesion these targets in arbitrary patterns for neuroscience research. See Hayes et al 2012 for an example of its usage (http://www.pnas.org/content/109/21/8286.abstract). -
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pyisocalc
Isotopic pattern calculator in python 2.x
This is an isotopic pattern calculator written in python. It depends on re, sys, numpy, operator, itertools, and matplotlib. -
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Mapnik is an OpenSource C++/Python toolkit for developing GIS (Geographic Information Systems) applications. At the core is a C++ shared library providing algorithms/patterns for spatial data access and visualization.
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Simple python code that produces color-coded quality plots based on fastq format read quality scores. Scores are averaged over binned read tile coordinates. Useful for spotting spatial quality patterns.
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Unique finds patterns in source code. It helps you build better software by finding pieces of code that could benefit from a refactoring.
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CodeIgor makes copies of given files, substituting user-defined patterns for given values. Every copy is related to a scpecific 'solution', so that you may define different versions of the same file, having the same patterns but different values.
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A library and associated applications for searching for patterns in protein structures and measuring geometric parameters.
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python enteprise integration framework project. Powerfull class library based on EAI patterns and a modeling and simulation tool.
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