Search Results for "data structure" - Page 5
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Showing 217 open source projects for "data structure"
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VSViewer3D
3D Virtual Screening Viewer
This project is an interactive viewer for 3D virtual screening data. -
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Immutable Collections for Java
Immutable/Persistent Collections Library
...A utility class provides functional style algorithmic processing of Cursors including foldLeft, foldRight, collect, select, and reject. The 2-3 tree and integer trie classes are optimized for performance and can be used alongside java.util Collections when immutability is needed for safe data sharing. -
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...Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the genome of target cells. We process around 1500 samples/year resulting in hundreds of millions of sequencing reads, requiring automation and posing new challenges in data storage, monitoring of sample process and computational tools for analyses. Thus we need to standardize data management and tracking systems, built on a scalable, flexible structure with an easily accessible and web based interface, what is usually called Laboratory Information Management System (LIMS). -
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Importer library to import assets from different common 3D file formats such as Collada, Blend, Obj, X, 3DS, LWO, MD5, MD2, MD3, MDL, MS3D and a lot of other formats. The data is stored in an own in-memory data-format, which can be easily processed. www.open3mod.com/ is a 3D model viewer and exporter based on Assimp that is also Open Source.
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XML Content Provider
Plugin to connect XML data sources to the GIN Server
The GIN Server is a semantic middleware for efficient "bottom-up" data integration and automized semantic analysis for dynamically linked data. The XML Content Provider is a configurable plugin for the GIN Server to integrate any XML data source with a simple structure. -
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Calculates Natural Product(NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. NP-likeness is a useful criterion to screen compound libraries and to design new lead compounds. Maven dependancy: <dependency> <groupId>uk.ac.ebi.cheminformatics</groupId> <artifactId>NP-Likeness</artifactId> <version>2.1</version> </dependency> Required repository: <repositories> ...
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SecStAnT
Secondary Structure Analysis Tool for data selection and statistics
SecStAnT is a tool for the automatic creation of data-sets of structures from Protein Data Bank (PDB) with user-defined structural composition, and for the calculation of their internal variables distributions. SecStAnT is able to 1. Select from PDB data sets of structures based on user specified secondary structures (defined based on internal PDB classification or on DSSP) and/or sequence motives. 2. Build Data-sets at different levels of resolution (all atoms, only backbone, only... -
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Unsupervised TXT classifier
Classify any two TXT documents, no training required - JAVA
...This extracts a relevant structure for both documents (and thus avoids the over-training) which are then compared using the Vector-Space analysis to give a range of belonging of one document to another (and thus avoids the shortage of information). This method can be used to create the user-defined classes by merging texts of certain categories and then to calculate the relevant distances between the documents, but this is not necessary. -
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Database to CSV
"Database to CSV" project stores/loads data between database and CSVs
"Database to CSV" allows to back-up data from database(Oracle, MySQL, SQL Server) in the form of CSV files. Each table data is stored in a separate CSV file. It also allows to load data from CSV files into the database. Program can be run from UI or from command line. There's one more advanced feature which allows merging of data from CSV file to Database. It is only available from command line. (It will take foreign keys and unique keys into consideration and then try to insert... -
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KochCurve
This small library implements a data structure for Koch curves.
This small library implements the Koch curve, snowflake and anti-snowflake like a Shape to be used like any other Java shape. You can test the library by compiling the test applet in Files. -
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Systems Glycobiology
Glycosylation Network Analysis Toolbox (GNAT)
...The original GNAT package (file GNAT.zip) provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks (citation [1]). The second version of this software (GNATv2beta.zip) upgrades the original GNAT program with additional features that are geared towards incorporating glycan-structure experimental data into the simulation environment. For information about GNAT installation and usage, please see the GettingStarted.pdf file enclosed in the package. To cite GNAT: [1] Gang Liu, Apurv Puri and Sriram Neelamegham, Glycosylation Network Analysis Toolbox (GNAT): a MATLAB based environment for systems glycobiology, Bioinformatics 2013 29: 404-406 -
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Stand-alone Java library implementing parser/formatter/comparator/validator for JSON/XML-like text formats oriented on JSON-like object model (list,map,scalar + reflection). Library is designed to maximize adaptivity via set of extendable modules.
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*** IMPORTANT NOTICE *** The source code of the earliest version of the EARMARK Data Structure is now available at http://www.github.com/essepuntato/EarmarkDataStructure Even if the SourceForge repository is still active, it concerns old versions of the API and it is not maintained anymore. *** SERVICE DESCRIPTION *** Extremely Annotational RDF Markup (EARMARK) is an ontological approach to the specification of markup structures on text content.
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Digital Content Component (DCC) is a self-descriptive unit to encapsulate any kind of content artifact. Designed to be reused and adapted, DCCs encapsulate data and software using a single structure.
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YAFF (Yet Another Factory Framework)
A Powerful Java Factory Framework
A Powerful Java Factory Framework -
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Predyketide is a stand-alone desktop application which provides a way to observe the resulting structure per elongation of the polyketide chain, and predict the most possible natural product structure. This tool can be helpful in the discovery of new drugs requiring lesser time and effort. The project uses the cdk v.1.5 and cdk-jchempaint-26.
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Java HTTP REST interface
Base for HTTP-REST Java application
Simplified multithreaded Java HTTP server able to interpret GET/POST requests. Example dummy app included. It uses Apache2 as a proxy for AJAX calls and jQuery code as a client. ------- Requirements: For the Java HTTP server: - J2SE (SDK for compilation) For the exampe web app: - Apache2 with mod_rewrite and mod_proxy Client-side for the web app: - www browser supporting JS with jQuery --- Setup: - run Server.class from Java server files (java Server) in a... -
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SW2PSA
SW2PSA (Stop & Wait and Sliding Window Protocol Simulator and Animator
...Since it is an open source program also helps the student who wishes to know the structure of a simple discrete event network simulator. -
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AdPreqFr4SL
Adaptive Prequential Learning Framework
The AdPreqFr4SL learning framework for Bayesian Network Classifiers is designed to handle the cost / performance trade-off and cope with concept drift. Our strategy for incorporating new data is based on bias management and gradual adaptation. Starting with the simple Naive Bayes, we scale up the complexity by gradually updating attributes and structure. Since updating the structure is a costly task, we use new data to primarily adapt the parameters and only if this is really necessary, do we adapt the structure. The method for handling concept drift is based on the Shewhart P-Chart. ... -
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IOS6 and recent iTunes updates have broken a few features. We have made some partial fixes, but they are not complete. If you'd like to help support our development, or take over the development please let us know. Explore the internal file structure of your iphone (or of a seized phone in the case of forensic teams) using either the iphone's own backup files or (for jail broken iphones) ssh. Viewing of plist, sqlite, and hex are supported. IOS 5 is now supported iOS 6 only partially...
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MySQLJavaBackup
Java Library for backing up MySQL Databases.
Use this library to backup your MySQL Database from your Java code. This library only backs up the data, not the database structure(Future Releases). So when restoring the backup file, you must ensure that the database is created and fully functional. -
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CUO
Codon Usage Optimizer
...The future plan for CUO is to be developed into a multipurpose bioinformatics software where data, findings, planning and learning in biology labs can be created and shared at finger tips. -
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RELATED - REmotes LAboraTories extenED
Java Framework for developing of remote/virtual laboratories
RELATED framework proposes a structured methodology of remote/virtual labs development and, also, provides common facilities as user management, booking, basic visualization (trend graphs and direct interaction using interactives variables), data logging and experimental session’s control. In order to get these facilities, an RLAB (Remote LABoratory) system it defined using a formal specification of a virtual or remote laboratory (based on XML and used to structure components for laboratory). The main component is experiment, so students could run these experiments using RELATED facilities as painting data from the laboratory, change any relevant variable or take a look on laboratory structure. ... -
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FreeFuzzyTime
It's a time reasoner that can be integrated in medical applications.
FuzzyTime module is a time reasoner base on Fuzzy Temporal Constraint Networks (FTCN) which treats fuzzy temporal information efficiently. It can be integrated into applications for diagnosis. This is especially important in areas like Intesive Care Units where patients' data are handled by a temporal data base. The FuzzyTime module is a structure which consists of three levels of abstraction. The upper layer is the user interface where a translator transforms the expressions introduced by the user into temporal relations between temporal entities (points and intervals). The semantic of user’s expressions is analized and stored in the intermediate layer or temporal world. ... -
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The idea behind this project is to design a website database structure, language-independent and build & link the CRUD pages needed to manipulate this data consistently in a specific language (jsp, php, or another), the same applies for the DB manager.
