Open Source Algorithms - Page 17

COPE (Connecting Overlapped Pair-End reads) is a method to align and connect the illumina sequenced Pair-End reads of which the insert size is smaller than the sum of the two read length.The connected reads can be used in genome assembly, resequencing and transcriptome research. The full citation: COPE: An accurate k-mer based pair-end reads connection tool to facilitate genome assembly Binghang Liu; Jianying Yuan; Siu-Ming Yiu; Zhenyu Li; Yinlong Xie; Yanxiang Chen; Yujian Shi; Hao Zhang; Yingrui Li; Tak-Wah Lam; Ruibang Luo Bioinformatics (2012) 28(22): 2870-2874; doi: 10.1093/bioinformatics/bts563

CRCLIB is a small library of CRC calculations which can be used in other programs. Because CRC check is often used by binary communication protocols, it is made as simple as it can be, built into library so that it could be used regardless of language of application code. Written in plain C, built as dll and static library, and also contains C/C++ import header, C# wrapper and .NET project for MS SQL Server assembly. Supports CRC16 (including MODBUS) and CRC32.

CRUSH is a pioneering reduction and imaging suite for many astronomical cameras operating at far-infrared, submillimeter and millimeter wavelengths, such as SHARC-2, SCUBA-2, LABOCA, GISMO, or SOFIA/HAWC+ (to name a few).

20 SkipList containers for C++ that work with STL. Combines set/map functionality with random access in logn time. One container is a multilist where you can order the same elements in a variety of different ways simultaneously.

CSGraph is a simple graph library. It provides the most popular algorithms to create and manipulate graphs.

Cascading and Sharing Survival Trees (CSST) is a tree-based enseble that allows to efficiently analize survival data. It is a strightforward extension of the CS4 method for lifetime collections of data. The CSST software comes along with its companion the CSST Prediction tool, to use the ensemble prediction in everyday life. Please, refer to the user's manual for further information.

CSTL is a port of the C++ STL to C# 2.0 and .NET. The library utilizes C# generics, anonymous methods, and enumerable iterators, while alleviating some of C#'s deficiencies (no C++ templates, limited operator overloading, no C++ style iterators, etc).

Implementation of cache conscious STL lists in Frias, L., Petit, J., and Roura, S. 2009. Lists revisited: Cache-conscious STL lists. J. Exp. Algorithmics 14 (Dec. 2009), 3.5-3.27. DOI= http://doi.acm.org/10.1145/1498698.1564505

Calamari is a collection of Java APIs for implementing genetic algorithms, neural networks, and vehicle simulation. It is still being designed and developed.

A capsule tree is a general purpose, self-balancing tree data structure for large, ordered, data-sets. It is designed to provide the same characteristics as B-trees and B+trees, but built from the ground up for in-memory usage. In other words, there are no provisions for “slow” I/O cases. The original motivation for this tree was a better backend for memory managers. However, the end result was a new sub-category of trees. The implementation giving here is just one implementation of the new tree sub-category, there can be others. In any case, read the PDF: “Capsule Trees - A Primer”, before delving into the code.

Find case inconsistencies in the source tree. May be useful for porting applications in any programming language from case-insensitive (like Windows) to case-sensitive (like Linux) runtime environment.

The Catalsyt Framework is a refinement on the MVC framework. It provides greater focus on user business workflow rather than application workflow. It's goal is to enable business analysis and developers to work closer.

Celluster is an easy adaptable producer/consumer software for distributed computing on a cluster of Cell B.E. processors

ChIPOTle 2.0 is a user friendly tool for performing peak detection in ChIP-chip signal. The tool also has functions for probe sorting, signal normalization, replication merging, and multiple correction testing in a windows interface or *nix command line.

A tool to represent Chapin diagrams

Fast search using a standard SQL on Oracle or PostgreSQL database. The package includes the database creator, loader and web application. It supports SMILES and SMARTS substructure searches, similarity search, stereochemistry.

Given a placement of pieces on a chessboard, find the move which forces checkmate as rapidly as possible.

This sofware is designed to help different chess clubs to set up their own rating system. It uses USCF approximation formulas for rating calculations. Working example at newarkcc.vfutbole.ru

KTDictSeg is a Chinese Segment Open source Project.

Hasher is a .NET class library to help programmers implement standard hashing and checksum algorithms into their own software. Written entirely in C#, Hasher providers a uniform interface to easily use any of the algorithms contained within this library

An experimental language designed to be very simple, but expressive enough to represent mathematical constructions and have strong introspective capabilities.

A C++ library for clipping polygons.

Clone Digger is a duplicate code detection tool, which supports Python and Java languages. Discovered clones can differ in small subexpressions; comments and whitespaces are ignored. Clone digger is platform-independent and is written in Python language

CoPP is an object-oriented framework for developing algorithms for robot path planning. One of of the design goals is to make it easy to make comparisons between various path planning algorithms.

Coach is a python framework that models the interaction between an agent and an environment in a modular way. With Coach, it is possible to model an agent by combining various building blocks, and training the agent on multiple environments. The available environments allow testing the agent in different fields such as robotics, autonomous driving, games and more. It exposes a set of easy-to-use APIs for experimenting with new RL algorithms and allows simple integration of new environments to solve. Coach collects statistics from the training process and supports advanced visualization techniques for debugging the agent being trained. Coach supports many state-of-the-art reinforcement learning algorithms, which are separated into three main classes - value optimization, policy optimization, and imitation learning. Coach supports a large number of environments which can be solved using reinforcement learning.