Sphere surface layers of visual cortex approach maximum info density
Near the surface (even horizon) of a black hole, there is maximum information density in units of squared plancks (and some translation to qubits). Similarly, our imagination is the set of all possible things we can draw onto our most dense layer of visual cortex in electricity patterns. Bigger layers have more neurons to handle those possibilities. A Black Hole Cortex is a kind of visual cortex that has density of neuron layers similar to density at various radius from a black hole. What we think our eyes see, the imagination, is the densest and smallest layer. SphereSurfaces outside it recursively have more neurons, more surface area, but less density since it has to eventually dimension-reduce to high level ideas, like there are 10000 Wikipedia page names that cover most parts of the world. We can think of Wikipedia as a layer above our brains, a global SphereSurface of large surface area (a cortex layered on billions of minds) and small (10000 most important pages) density.
A population-based method for DNA copy number analysis: recurrent copy number aberration indentification in multiple samples (with no need of single-sample calling). Developed for a quick analysis of high resolution and large population data.
Differential Expression Analysis for Pathways
This project contains the source code associated with the PLoS Computational Biology publication: "Differential Expression Analysis for Pathways". The paper text can be found here: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002967
MLE survival analysis: Gompertz, Weibull, Logistic and mixed morality.
DeDAY (Demography Data Analyses) is a tool of analyzing demography data. It supports Gompertz, Weibull and Logistic distributions. DeDay also supports mixed mortality models based on these distribution such as the Gompertz-Makeham distribution. Distributions such as Gompertz describes only age-dependent mortality, which increases over time. Mixed mortality models, such as in Gompertz-Makeham distribution, consider a more general case where mortality is consist of both age-dependent and in-dependent mortality. Mixed models partition mortality into exogenous and endogenous components, so that the intrinsic survivorship can be estimated without the interference from extrinsic noise. DeDAY supports both interval-censored data and exact event-time data. Using MLE (Maximum Likelihood Estimate), DeDAY fits statistic model to the data. DeDAY also calculates the variances and the multi-dimensional confidence limits of model parameters. DeDAY is free for academic users.
An R Package for Environmental Statistics
EnvStats is an R package for environmental statistics. It is the open-source successor to the commercial module for S-Plus© called "EnvironmentalStats for S-Plus", which was first released in April, 1997. The EnvStats package, along with the R software environment, provides comprehensive and powerful software for environmental data analysis. EnvStats brings the major environmental statistical methods found in the literature and regulatory guidance documents into one statistical package, along with an extensive hypertext help system that explains what these methods do, how to use these methods, and where to find them in the environmental statistics literature. Also included are numerous built-in data sets from regulatory guidance documents and the environmental statistics literature. EnvStats combined with other R packages (e.g., for spatial analysis) provides the environmental scientist, statistician, researcher, and technician with tools to “get the job done!”
MORphological PHenotype Extraction
MORphological PHenotype Extraction (MORPHE) is a suite of automated image processing, visualization, and classification algorithms to facilitate the analysis of heritable and clonal red-to-green transitions that occurred during the growth of a colony.
neural network implementation in java
3-layer neural network for regression and classification with sigmoid activation function and command line interface similar to LibSVM. Quick Start: "java -jar nen.jar"
Calculates the Type Token Ratio (Expressive Vocabulary) in any text.
Novel Score will calculate an approximate TTR (Type Token Ratio) of any standard text. Simply copy and paste, then analyze. Novel Score will also get gather and rank said text's most commonly used words. This tool was originally built to analyze the word variance of different authors. To a certain extent, TTR is a measure of one's expressive vocabulary, and thus writing ability. However, take any results with a grain of salt.
Synchronous Petri Nets' emulator
QPNet (Quick Petri Net) is a fast Petri Nets' emulator, created by students of Moscow State Technical University of Radio Engineering, Electronics and Automation. It brings benefits for the educational process, while being under further development and extension. QPNet это быстрый эмулятор сетей Петри, созданный студентами МИРЭА. Он применяется в учебном процессе, а так же продолжает разрабатываться и эволюционировать.
* GSA-SNP2 is a successor of GSA-SNP (Nam et al. 2010, NAR web server issue). GSA-SNP2 accepts human GWAS summary data (rs numbers, p-values) or gene-wise p-values (possibly obtained from VEGAS or GATES) and outputs pathway gene sets ‘enriched’ with genes associated with the given phenotype. It also provides both local and global protein interaction networks in the associated pathways. * IMPORTANT NOTE: -> PLEASE MOVE OR MAKE A COPY OF 'DATA' FOLDER INTO YOUR INTENSIVE TEST FOLDER (I.E. LINUX OR MAC OR WINDOWS SPECIFIED FOLDER) TO ALLOW THE PROGRAM TO FIND THE PREDESIGNED DATA. * UPDATE NOTE: -> Jan-8-2018: minor output format update for all versions -> Aug-4-2017: minor bugs fixed: i/o bugs do not load input from GO and KEGG radio options -> Apr-3-2017: MacOSX command-line version is added. It also provides the PPI net summarization -> Mar-31-2017: Linux and Windows command-line versions now provide the PPI net summary results (except the net visualization)
R package for hierarchical species distribution models
hSDM is an R package for hierarchical species distribution models. Such models allows interpreting the observations (occurrence and abundance of a species) as a result of several hierarchical processes including ecological processes (habitat suitability, spatial dependence and anthropogenic disturbance) and observation processes (species detectability). Hierarchical species distribution models are essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results.
Library for optimization using a genetic algorithm or particle swarms
libfgen is a library that implements an efficient and customizable genetic algorithm (GA). It also provides particle swarm optimization (PSO) functionality and an interface for real-valued function minimization or model fitting. It is written in C, but can also be compiled with a C++ compiler. Both Linux and Windows are supported.
This is a Matlab software package for single molecule FRET data analysis.
An R package to normalise, classify and analyses raw AFLP data.
Arredondamento de Números
Sistema de Apoio Didático Profissional. ARNU - Arredondamento de Números. O aplicativo ARNU tem por objetivo auxiliar na resolução de cálculos de arredondamento matemático, abordados de forma técnica, entregando ao usuário um resultado didático e objetivo, o motivo e as normas utilizadas.
Actuarial Visual Web environment. Computer Sciences Actuarial Mathematic Object Library and GUI. Non-linear stochastic asset model and linear asset models for actuarial use.
A alternative to the SAS Viewer written in SAS/AF. First presented on 2010-10-05 in BASAS meeting. With extended abilities in sorting, filtering, simple frequency count, statistics and various data review oriented features.
ARO helps physically disabled students to create mathematical drawings
ARO has been developed to assist physically disabled or injured students who cannot create mathematical drawings on paper. It is intended to make maths up to Key Stage 4 more accessible. AQA has agreed to its use in a GCSE maths exam. Anyone who can use a computer with a mouse to access the internet should be able to use ARO. The processes required mimic those of on paper drawing as far as possible. Possible applications include: Graphs of straight lines and smooth curves Compass and ruler constructions Scatter graphs Stem and leaf displays Box plots Histograms Pie charts Simple diagrams. The structure of each drawing is built from individual components which can be placed on the drawing grid without great accuracy. Each can then be positioned exactly using onscreen buttons. The ruler and the protractor can be aligned with any straight line. Drawings can be created on imported background bitmaps. The author was a mathematics lecturer at Plymouth University.
BIL++ is a set of standalone C++ packages for data processing in Bioinformatics (Graph mining, Bayesian networks, Genetic algorithm, Discretization, Gene expression data analysis, Hypothesis testing).
BigBang/Horizon is a proteomics data analysis pipeline with focus on the shotgun LC/MSMS workflow.
A simple to use Binomial Distribution Calculator.
A simple to use binomial distribution calculator: Just enter the sufficient data like number of trials, probability and number of successes. You can display the calculated data in a table or even graphically. Simultaneously, this application computes the expected value and the standard deviation. To use this app you need to have .NET Framework 4 installed. Contact me: email@example.com
BAYESIAN INFERENCE OF METABOLIC DIVERGENCE AMONG MICROBIAL COMMUNITIES
Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function. Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework. Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic networks among microbial communities. To infer the structure of community-level metabolic interactions, BiomeNet applies a mixed-membership modelling framework to enzyme abundance information. The basic idea is that the mixture components of the model (metabolic reactions, subnetworks, and networks) are shared across all groups (microbiome samples), but the mixture proportions vary from group to group. Through this framework, the model can capture nested structures within the data. BiomeNet is unique in modeling each metagenome sample as a mixture of complex metabolic systems (metabosystems).
A collection of different methods for implementing in C++ polycrystalline growth for metals during annealing or recrystallization.
That project aims at providing a clean API and a simple implementation, as a C++ library, of an Airline-related Inventory Management system. That library uses the Standard Airline IT C++ object model (http://sf.net/projects/stdair).
A Multivariate Distributions Package for C++
A library based on Eigen and Boost to handle common multivariate distributions in C++