An Open Source performance tools software suite for scientific computing

2009 ◽  
pp. n/a-n/a
Author(s):  
Philip J. Mucci ◽  
Tushar Mohan
Keyword(s):  
Open Source ◽  
Scientific Computing ◽  
Software Suite

scholarly journals Jupyter: Thinking and Storytelling with Code and Data

2021 ◽  
Author(s):  
Brian Granger ◽  
Fernando Pérez
Keyword(s):  
Machine Learning ◽  
Open Source ◽  
Community Of Practice ◽  
Scientific Computing ◽  
Data Science ◽  
Climate Science ◽  
Three Dimensions ◽  
Open Source Project ◽  
Interactive Computing ◽  
The Impact

Project Jupyter is an open-source project for interactive computing widely used in data science, machine learning, and scientific computing. We argue that even though Jupyter helps users perform complex, technical work, Jupyter itself solves problems that are fundamentally human in nature. Namely, Jupyter helps humans to think and tell stories with code and data. We illustrate this by describing three dimensions of Jupyter: interactive computing, computational narratives, and  the idea that Jupyter is more than software. We illustrate the impact of these dimensions on a community of practice in Earth and climate science.

itom – An Open Source Measurement, Automation and Evaluation Software Suite

Fringe 2013 ◽  
2014 ◽  
pp. 957-964
Author(s):  
Marc Gronle ◽  
Christian Kohler ◽  
Marc Wilke ◽  
Wolfram Lyda ◽  
Heiko Bieger ◽  
...  
Keyword(s):  
Open Source ◽  
Software Suite ◽  
Measurement Automation

scholarly journals The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development

2019 ◽  
Vol 16 (3) ◽  
Author(s):  
Bjorn Sommer
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Biological Networks ◽  
Special Focus ◽  
Database Integration ◽  
Software Suite ◽  
Software Frameworks ◽  
Cell Components ◽  
History Of ◽  
Student Projects

AbstractFor more than one decade, CELLmicrocosmos tools are being developed. Here, we discus some of the technical and administrative hurdles to keep a software suite running so many years. The tools were being developed during a number of student projects and theses, whereas main developers refactored and maintained the code over the years. The focus of this publication is laid on two Java-based Open Source Software frameworks. Firstly, the CellExplorer with the PathwayIntegration combines the mesoscopic and the functional level by mapping biological networks onto cell components using database integration. Secondly, the MembraneEditor enables users to generate membranes of different lipid and protein compositions using the PDB format. Technicalities will be discussed as well as the historical development of these tools with a special focus on group-based development. In this way, university-associated developers of Integrative Bioinformatics applications should be inspired to go similar ways. All tools discussed in this publication can be downloaded and installed from https://www.CELLmicrocosmos.org.

The MetaProteomeAnalyzer: A Powerful Open-Source Software Suite for Metaproteomics Data Analysis and Interpretation

2015 ◽  
Vol 14 (3) ◽  
pp. 1557-1565 ◽  
Author(s):  
Thilo Muth ◽  
Alexander Behne ◽  
Robert Heyer ◽  
Fabian Kohrs ◽  
Dirk Benndorf ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Software Suite

scholarly journals pMAT: An Open-Source Software Suite for the Analysis of Fiber Photometry Data

2020 ◽  
pp. 173093
Author(s):  
Carissa A. Bruno ◽  
Chris O’Brien ◽  
Svetlana Bryant ◽  
Jennifer Mejaes ◽  
David J. Estrin ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Suite

A SonarQube Static Analysis of the Spectral Workbench

2021 ◽  
pp. 16
Author(s):  
Keyword(s):  
Data Collection ◽  
Open Source ◽  
Spectral Data ◽  
Static Analysis ◽  
Analysis Tool ◽  
Client Application ◽  
Online Database ◽  
Software Suite ◽  
Server Application ◽  
Static Analysis Tool

The Spectral Workbench is an open-source, community driven software suite to obtain and disseminate spectral data. It consists of a client application that collects spectral readings and a server application that is an online database of spectral data. It is difficult to detect software defects in the Spectral Workbench application. A static analysis tool, SonarQube, was selected to find these defects. Numerous defects were detected and documented. SonarQube will increase the reliability of the Spectral Workbench, which provides numerous benefits including increased confidence in its data and effectiveness which will drive additional number of users for spectral repository data collection.

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