Modular Toolkit for Data Processing (MDP): A Python Data Processing Framework

Modular toolkit for Data Processing (MDP) is a data processing framework written in Python. From the user's perspective, MDP is a collection of supervised and unsupervised learning algorithms and other data processing units that can be combined into data processing sequences and more complex feed-forward network architectures. Computations are performed efficiently in terms of speed and memory requirements. From the scientific developer's perspective, MDP is a modular framework, which can easily be expanded. The implementation of new algorithms is easy and intuitive. The new implemented units are then automatically integrated with the rest of the library. MDP has been written in the context of theoretical research in neuroscience, but it has been designed to be helpful in any context where trainable data processing algorithms are used. Its simplicity on the user's side, the variety of readily available algorithms, and the reusability of the implemented units make it also a useful educational tool

Flow: Statistics, visualization and informatics for flow cytometry

Flow is an open source software application for clinical and experimental researchers to perform exploratory data analysis, clustering and annotation of flow cytometric data. Flow is an extensible system that offers the ease of use commonly found in commercial flow cytometry software packages and the statistical power of academic packages like the R BioConductor project

Scikit-learn: Machine Learning in Python

International audienceScikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from http://scikit-learn.sourceforge.net

Robotics Middleware: A Comprehensive Literature Survey and Attribute-Based Bibliography

Autonomous robots are complex systems that require the interaction between numerous heterogeneous components (software and hardware). Because of the increase in complexity of robotic applications and the diverse range of hardware, robotic middleware is designed to manage the complexity and heterogeneity of the hardware and applications, promote the integration of new technologies, simplify software design, hide the complexity of low-level communication and the sensor heterogeneity of the sensors, improve software quality, reuse robotic software infrastructure across multiple research efforts, and to reduce production costs. This paper presents a literature survey and attribute-based bibliography of the current state of the art in robotic middleware design. The main aim of the survey is to assist robotic middleware researchers in evaluating the strengths and weaknesses of current approaches and their appropriateness for their applications. Furthermore, we provide a comprehensive set of appropriate bibliographic references that are classified based on middleware attributes.http://dx.doi.org/10.1155/2012/95901

OpenElectrophy: An Electrophysiological Data- and Analysis-Sharing Framework

Progress in experimental tools and design is allowing the acquisition of increasingly large datasets. Storage, manipulation and efficient analyses of such large amounts of data is now a primary issue. We present OpenElectrophy, an electrophysiological data- and analysis-sharing framework developed to fill this niche. It stores all experiment data and meta-data in a single central MySQL database, and provides a graphic user interface to visualize and explore the data, and a library of functions for user analysis scripting in Python. It implements multiple spike-sorting methods, and oscillation detection based on the ridge extraction methods due to Roux et al. (2007). OpenElectrophy is open source and is freely available for download at http://neuralensemble.org/trac/OpenElectrophy

Towards a Reference Architecture with Modular Design for Large-scale Genotyping and Phenotyping Data Analysis: A Case Study with Image Data

With the rapid advancement of computing technologies, various scientific research communities have been extensively using cloud-based software tools or applications. Cloud-based applications allow users to access software applications from web browsers while relieving them from the installation of any software applications in their desktop environment. For example, Galaxy, GenAP, and iPlant Colaborative are popular cloud-based systems for scientific workflow analysis in the domain of plant Genotyping and Phenotyping. These systems are being used for conducting research, devising new techniques, and sharing the computer assisted analysis results among collaborators. Researchers need to integrate their new workflows/pipelines, tools or techniques with the base system over time. Moreover, large scale data need to be processed within the time-line for more effective analysis. Recently, Big Data technologies are emerging for facilitating large scale data processing with commodity hardware. Among the above-mentioned systems, GenAp is utilizing the Big Data technologies for specific cases only. The structure of such a cloud-based system is highly variable and complex in nature. Software architects and developers need to consider totally different properties and challenges during the development and maintenance phases compared to the traditional business/service oriented systems. Recent studies report that software engineers and data engineers confront challenges to develop analytic tools for supporting large scale and heterogeneous data analysis. Unfortunately, less focus has been given by the software researchers to devise a well-defined methodology and frameworks for flexible design of a cloud system for the Genotyping and Phenotyping domain. To that end, more effective design methodologies and frameworks are an urgent need for cloud based Genotyping and Phenotyping analysis system development that also supports large scale data processing. In our thesis, we conduct a few studies in order to devise a stable reference architecture and modularity model for the software developers and data engineers in the domain of Genotyping and Phenotyping. In the first study, we analyze the architectural changes of existing candidate systems to find out the stability issues. Then, we extract architectural patterns of the candidate systems and propose a conceptual reference architectural model. Finally, we present a case study on the modularity of computation-intensive tasks as an extension of the data-centric development. We show that the data-centric modularity model is at the core of the flexible development of a Genotyping and Phenotyping analysis system. Our proposed model and case study with thousands of images provide a useful knowledge-base for software researchers, developers, and data engineers for cloud based Genotyping and Phenotyping analysis system development

ASL Fingerspelling Recognition Using Slow Feature Analysis

Táto práca popisuje proces testovania slow feature analysis ako metódy, ktorá extrahuje robustné črty z komplexných obrazových dát americkej znakovej reči. Za účelom testovania bol vytvorený systém v programovacom jazyku python, ktorý zjednodušuje testovanie a ponúka bohatú škálu meniteľných parametrov aby umožnil užívateľovi rôzne testy za účelom zistenia nakoľko použiteľná je táto metóda na klasifikáciu a rozpoznávanie gest rúk. Teoretická časť predstaví slow feature analysis, diskutuje o štruktúre systému a popisuje dáta na ktorých bude metóda pozorovaná. V praktickej časti je metóda podrobená analýze úspešnosti na videných a nevidených rečníkoch, jej schopnosť adaptovať sa na vyšší počet gest a zaujímavé formátovanie dát v pokuse vylepšiť jej úspešnosť.This work describes the process of testing slow feature analysis as a method of extracting rhobust features from complex image data of american sign language. For purposes of testing a system in python is created that facilitates test runs and offers rich scale of changable specifications to allow the user run various tests in order to determine how viable the method is for classification and recognition of hand shapes. The theoretical part introduces the slow feature analysis, discusses the structure of the system and describes the dataset on which the method is to be observed. In practical part the method was subjected to performance analysis on seen and unseen speakers, its viability with higher number of gestures and some interesting input data formatting in attempt to improve the performance.