scholarly journals FACSanadu: Graphical user interface for rapid visualization and quantification of flow cytometry data

2017 ◽  
Author(s):  
T.R. Bürglin ◽  
J. Henriksson
Keyword(s):  
Flow Cytometry ◽  
Open Source ◽  
Operating Systems ◽  
Graphical User Interface ◽  
Cell Biology ◽  
Source Code ◽  
Free Software ◽  
Read Length ◽  
Profile Data ◽  
Flow Cytometry Data

ABSTRACTMotivationFlow cytometry is a fundamental technique in cell biology, yet few open source packages are available to analyse these data. Here we describe FACSanadu, an interactive package for rapid visualization and measurement of flow cytometry data. It is the first open source package that can read length profile data from the COPAS Biosorter.Availability and ImplementationFACSanadu is implemented in Java and uses the Qt framework for display. Binary distributions are made for all major operating systems (Windows, Macintosh, Linux). The source code and documentation is available as free software at http://www.facsanadu.org.Contact:[email protected]

scholarly journals GeoEasy an open source project for surveying calculations

2018 ◽  
Vol 17 (2) ◽  
pp. 1-8 ◽  
Author(s):  
Zoltan Siki
Keyword(s):  
Operating System ◽  
User Interface ◽  
Open Source ◽  
Operating Systems ◽  
Graphical User Interface ◽  
Free Software ◽  
Script Language ◽  
The Core ◽  
User Friendly ◽  
Friendly Graphical User Interface

The development of the GeoEasy program started in 1997. Twenty years later in 2017 it became free software under GPL license, version 3.0.0 is freely available for everybody. The core development of GeoEasy is made on Linux operating system, using Tcl/Tk script language, thanks to the Tcl/Tk ports to other operating systems, the program can be run on Linux, Windows, Android and OSX machines. Objectives of the development are to create user friendly graphical user interface (GUI) for surveying calculations in a modular structure with flexible, open connections to other programs. Both educational and professional usages are supported.

Open Source

2019 ◽  
pp. 1067-1075
Author(s):  
Heidi Lee Schnackenberg
Keyword(s):  
General Population ◽  
Open Source ◽  
Operating Systems ◽  
Open Source Software ◽  
Mobile Applications ◽  
Free Software ◽  
Free Products

The phrase “open source” is not something often heard in everyday conversation. However, the idea of downloadable, free software, particularly mobile applications, or “apps,” has become quite commonplace. Individuals often download free products, grateful that they are available and will potentially work well, without thinking where they originate or why they even exist. Not so long ago, most things associated with computers available to the general population came at a cost and were available from only a few vendors. This is no longer the case thanks to the ever-increasing availability and popularity of open source software, operating systems, and applications.

Open Source in Government

2011 ◽  
pp. 1287-1290 ◽  
Author(s):  
D. Berry
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
General Public ◽  
Source Code ◽  
Computer Software ◽  
Free Software ◽  
Software Projects ◽  
Software Companies ◽  
Develop Software ◽  
Software Distribution

Open source software (OSS) is computer software that has its underlying source code made available under a licence. This can allow developers and users to adapt and improve it (Raymond, 2001). Computer software can be broadly split into two development models: • Proprietary, or closed software, owned by a company or individual. Copies of the binary are made public; the source code is not usually made public. • Open-source software (OSS), where the source code is released with the binary. Users and developers can be licenced to use and modify the code, and to distribute any improvements they make. Both OSS and proprietary approaches allow companies to make a profit. Companies developing proprietary software make money by developing software and then selling licences to use the software. For example, Microsoft receives a payment for every copy of Windows sold with a personal computer. OSS companies make their money by providing services, such as advising clients on the GPL licence. The licencee can either charge a fee for this service or work free of charge. In practice, software companies often develop both types of software. OSS is developed by an ongoing, iterative process where people share the ideas expressed in the source code. The aim is that a large community of developers and users can contribute to the development of the code, check it for errors and bugs, and make the improved version available to others. Project management software is used to allow developers to keep track of the various versions. There are two main types of open-source licences (although there are many variants and subtypes developed by other companies): • Berkeley Software Distribution (BSD) Licence: This permits a licencee to “close” a version (by withholding the most recent modifications to the source code) and sell it as a proprietary product; • GNU General Public Licence (GNU, GPL, or GPL): Under this licence, licencees may not “close” versions. The licencee may modify, copy, and redistribute any derivative version, under the same GPL licence. The licencee can either charge a fee for this service or work free of charge. Free software first evolved during the 1970s but in the 1990s forked into two movements, namely free software and open source (Berry, 2004). Richard Stallman, an American software developer who believes that sharing source code and ideas is fundamental to freedom of speech, developed a free version of the widely used Unix operating system. The resulting GNU program was released under a specially created General Public Licence (GNU, GPL). This was designed to ensure that the source code would remain openly available to all. It was not intended to prevent commercial usage or distribution (Stallman, 2002). This approach was christened free software. In this context, free meant that anyone could modify the software. However, the term “free” was often misunderstood to mean no cost. Hence, during the 1990s, Eric Raymond and others proposed that open-source software was coined as a less contentious and more business-friendly term. This has become widely accepted within the software and business communities; however there are still arguments about the most appropriate term to use (Moody, 2002). The OSMs are usually organised into a network of individuals who work collaboratively on the Internet, developing major software projects that sometimes rival commercial software but are always committed to the production of quality alternatives to those produced by commercial companies (Raymond, 2001; Williams, 2002). Groups and individuals develop software to meet their own and others’ needs in a highly decentralised way, likened to a Bazaar (Raymond, 2001). These groups often make substantive value claims to support their projects and foster an ethic of community, collaboration, deliberation, and intellectual freedom. In addition, it is argued by Lessig (1999) that the FLOSS community can offer an inspiration in their commitment to transparency in their products and their ability to open up governmental regulation and control through free/libre and open source code.

scholarly journals FlowCal: A User-Friendly, Open Source Software Tool for Automatically Converting Flow Cytometry Data from Arbitrary to Calibrated Units

2016 ◽  
Vol 5 (7) ◽  
pp. 774-780 ◽  
Author(s):  
Sebastian M. Castillo-Hair ◽  
John T. Sexton ◽  
Brian P. Landry ◽  
Evan J. Olson ◽  
Oleg A. Igoshin ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Open Source ◽  
Open Source Software ◽  
Software Tool ◽  
Flow Cytometry Data ◽  
User Friendly

scholarly journals OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

2014 ◽  
Vol 10 (8) ◽  
pp. e1003806 ◽  
Author(s):  
Greg Finak ◽  
Jacob Frelinger ◽  
Wenxin Jiang ◽  
Evan W. Newell ◽  
John Ramey ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Data Analysis ◽  
Open Source ◽  
Flow Cytometry Data ◽  
End To End

scholarly journals A review of Open Source Software and Open Source Movement in Developing Countries

2011 ◽  
pp. 91-95
Author(s):  
Shyamalendu Kandar ◽  
Sourav Mondal ◽  
Palash Ray
Keyword(s):  
Developing Countries ◽  
Open Source ◽  
Open Source Software ◽  
Source Code ◽  
Computer Software ◽  
Free Software ◽  
Commercial Software ◽  
Large Organization ◽  
Software License ◽  
Indian Perspective

Open-source software abbreviated as OSS is computer software that is available with source code and is provided under a software license that permits users to study, change, and improve the software. For the commercial software the source code and certain other rights are normally reserved for copyright holders,i.e. the company who developes the software. A group of people in a collaborative manner often developes the Open source software, not under the roof of a large organization. This strategy makes open source software cheap, reliable and modifiable if needed. In this context we shall discuss mainly the features of Open Source Software, differences of open source and free software and open source software movement in Indian perspective.

scholarly journals An open-source solution for advanced imaging flow cytometry data analysis using machine learning

Methods ◽  
2017 ◽  
Vol 112 ◽  
pp. 201-210 ◽  
Author(s):  
Holger Hennig ◽  
Paul Rees ◽  
Thomas Blasi ◽  
Lee Kamentsky ◽  
Jane Hung ◽  
...  
Keyword(s):  
Machine Learning ◽  
Flow Cytometry ◽  
Data Analysis ◽  
Open Source ◽  
Advanced Imaging ◽  
Flow Cytometry Data ◽  
Imaging Flow Cytometry

scholarly journals FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data

2020 ◽  
Vol 9 (9) ◽  
pp. 2258-2266
Author(s):  
Alex J. H. Fedorec ◽  
Clare M. Robinson ◽  
Ke Yan Wen ◽  
Chris P. Barnes
Keyword(s):  
Flow Cytometry ◽  
Open Source ◽  
Open Source Software ◽  
Software Package ◽  
Flow Cytometry Data ◽  
Plate Reader ◽  
Open Source Software Package

scholarly journals The GridCAT: A toolbox for automated analysis of human grid cell codes in fMRI

2017 ◽  
Author(s):  
Matthias Stangl ◽  
Jonathan Shine ◽  
Thomas Wolbers
Keyword(s):  
User Interface ◽  
Open Source ◽  
Graphical User Interface ◽  
Cognitive Processes ◽  
Source Code ◽  
Research Area ◽  
List Type ◽  
Grid Cells ◽  
Code Analysis ◽  
Open Source Code

AbstractHuman fMRI studies examining the putative firing of grid cells (i.e., the grid code) suggest that this cellular mechanism supports not only spatial navigation, but also more abstract cognitive processes. This research area, however, remains relatively unexplored, perhaps us to the complexities of data analysis. To overcome this, we have developed the Matlab-based Grid Code Analysis Toolbox (GridCAT), providing a graphical user interface, and open-source code, for the analysis of fMRI data. The GridCAT performs all analyses, from estimation and fitting of the grid code in the general linear model, to the generation of grid code metrics and plots. Moreover, it is flexible in allowing the specification of bespoke analysis pipelines; example data are provided to demonstrate the GridCAT’s main functionality. We believe the GridCAT is essential to opening this research area to the imaging community, and helping to elucidate the role of human grid codes in higher-order cognitive processes.HighlightsThe putative firing of grid cells (i.e., the grid code) can be examined using fMRINecessary steps for grid code analysis are reviewedThe Matlab-based grid code analysis toolbox (GridCAT) is introducedAutomated grid code analysis can be conducted either via a graphical user interface or open-source codeA detailed manual and an example dataset are provided

Open Source in Government

2011 ◽  
pp. 1171-1176
Author(s):  
David Berry
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
General Public ◽  
Source Code ◽  
Computer Software ◽  
Free Software ◽  
Software Projects ◽  
Software Companies ◽  
Develop Software ◽  
Software Distribution

Open source software (OSS) is computer software that has its underlying source code made available under a licence. This can allow developers and users to adapt and improve it (Raymond, 2001). Computer software can be broadly split into two development models: • Proprietary, or closed software, owned by a company or individual. Copies of the binary are made public; the source code is not usually made public. • Open-source software (OSS), where the source code is released with the binary. Users and developers can be licenced to use and modify the code, and to distribute any improvements they make. Both OSS and proprietary approaches allow companies to make a profit. Companies developing proprietary software make money by developing software and then selling licences to use the software. For example, Microsoft receives a payment for every copy of Windows sold with a personal computer. OSS companies make their money by providing services, such as advising clients on the GPL licence. The licencee can either charge a fee for this service or work free of charge. In practice, software companies often develop both types of software. OSS is developed by an ongoing, iterative process where people share the ideas expressed in the source code. The aim is that a large community of developers and users can contribute to the development of the code, check it for errors and bugs, and make the improved version available to others. Project management software is used to allow developers to keep track of the various versions. There are two main types of open-source licences (although there are many variants and subtypes developed by other companies): • Berkeley Software Distribution (BSD) Licence: This permits a licencee to “close” a version (by withholding the most recent modifications to the source code) and sell it as a proprietary product; • GNU General Public Licence (GNU, GPL, or GPL): Under this licence, licencees may not “close” versions. The licencee may modify, copy, and redistribute any derivative version, under the same GPL licence. The licencee can either charge a fee for this service or work free of charge. Free software first evolved during the 1970s but in the 1990s forked into two movements, namely free software and open source (Berry, 2004). Richard Stallman, an American software developer who believes that sharing source code and ideas is fundamental to freedom of speech, developed a free version of the widely used Unix operating system. The resulting GNU program was released under a specially created General Public Licence (GNU, GPL). This was designed to ensure that the source code would remain openly available to all. It was not intended to prevent commercial usage or distribution (Stallman, 2002). This approach was christened free software. In this context, free meant that anyone could modify the software. However, the term “free” was often misunderstood to mean no cost. Hence, during the 1990s, Eric Raymond and others proposed that open-source software was coined as a less contentious and more business-friendly term. This has become widely accepted within the software and business communities; however there are still arguments about the most appropriate term to use (Moody, 2002). The OSMs are usually organised into a network of individuals who work collaboratively on the Internet, developing major software projects that sometimes rival commercial software but are always committed to the production of quality alternatives to those produced by commercial companies (Raymond, 2001; Williams, 2002). Groups and individuals develop software to meet their own and others’ needs in a highly decentralised way, likened to a Bazaar (Raymond, 2001). These groups often make substantive value claims to support their projects and foster an ethic of community, collaboration, deliberation, and intellectual freedom. In addition, it is argued by Lessig (1999) that the FLOSS community can offer an inspiration in their commitment to transparency in their products and their ability to open up governmental regulation and control through free/libre and open source code.

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