scholarly journals SpectraFox: A free open-source data management and analysis tool for scanning probe microscopy and spectroscopy

SoftwareX ◽  
2016 ◽  
Vol 5 ◽  
pp. 31-36 ◽  
Author(s):  
Michael Ruby
Author(s):  
Liguo Yu ◽  
David R. Surma ◽  
Hossein Hakimzadeh

Software development is a fast-changing area. New methods and new technologies emerge all the time. As a result, the education of software engineering is generally considered not to be keeping pace with the development of software engineering in industry. Given the limited resources in academia, it is unrealistic to purchase all the latest software tools for classroom usage. In this chapter, the authors describe how free/open-source data and free/open-source tools are used in an upper-level software engineering class at Indiana University South Bend. Depending on different learning objectives, different free/open-source tools and free/open-source data are incorporated into different team projects. The approach has been applied for two semesters, where instructor’s experiences are assembled and analyzed. The study suggests (1) incorporating both free/open-source tools and free/open-source data in a software engineering course so that students can better understand both development methods and development processes and (2) updating software engineering course regularly in order to keep up with the advance of development tools and development methods in industry.


Author(s):  
Liguo Yu ◽  
David R. Surma ◽  
Hossein Hakimzadeh

Software development is a fast-changing area. New methods and new technologies emerge all the time. As a result, the education of software engineering is generally considered not to be keeping pace with the development of software engineering in industry. Given the limited resources in academia, it is unrealistic to purchase all the latest software tools for classroom usage. In this chapter, the authors describe how free/open-source data and free/open-source tools are used in an upper-level software engineering class at Indiana University South Bend. Depending on different learning objectives, different free/open-source tools and free/open-source data are incorporated into different team projects. The approach has been applied for two semesters, where instructor's experiences are assembled and analyzed. The study suggests (1) incorporating both free/open-source tools and free/open-source data in a software engineering course so that students can better understand both development methods and development processes and (2) updating software engineering course regularly in order to keep up with the advance of development tools and development methods in industry.


2011 ◽  
Vol 12 (S7) ◽  
Author(s):  
Teeradache Viangteeravat ◽  
Venkateswara Ra Nagisetty ◽  
Matthew N Anyanwu ◽  
Emin Kuscu ◽  
Ian M Brooks ◽  
...  

2020 ◽  
Author(s):  
Louise Darroch ◽  
Juan Ward ◽  
Alexander Tate ◽  
Justin Buck

<div> <p>More than 40% of the human population live within 100 km of the sea. Many of these communities intimately rely on the oceans for their food, climate and economy. However, the oceans are increasingly being adversely affected by human-driven activities such as climate change and pollution. Many targeted, marine monitoring programmes (e.g. GOSHIP, OceanSITES) and pioneering observing technologies (e.g. autonomous underwater vehicles, Argo floats) are being used to assess the impact humans are having on our oceans. Such activities and platforms are deployed, calibrated and serviced by state-of-the-art research ships, multimillion-pound floating laboratories which operate diverse arrays of high-powered, high-resolution sensors around-the-clock (e.g. sea-floor depth, weather, ocean current velocity and hydrography etc.). These sensors, coupled with event and environmental metadata provided by the ships logs and crew, are essential for understanding the wider context of the science they support, as well as directly contributing to crucial scientific understanding of the marine environment and key strategic policies (e.g. United Nation’s Sustainable Development Goal 14). However, despite their high scientific value and cost, these data streams are not routinely brought together from UK large research vessels in coordinated, reliable and accessible ways that are fundamental to ensuring user trust in the data and any products generated from the data.  </p> </div><div> <p>The National Oceanography Centre (NOC) and British Antarctic Survey (BAS) are currently working together to improve the integrity of the data management workflow from sensor systems to end-users across the UK National Environment Research Council (NERC) large research vessel fleet, making cost effective use of vessel time while improving the FAIRness of data from these sensor arrays. The solution is based upon an Application Programming Interface (API) framework with endpoints tailored towards different end-users such as scientists on-board the vessels as well as the public on land. Key features include: Sensor triage using real-time automated monitoring systems, assuring sensors are working correctly and only the best data are output; Standardised digital event logging systems allowing data quality issues to be identified and resolved quickly; Novel open-source, data transport formats that are embedded with well-structured metadata, common standards and provenance information (such as controlled vocabularies and persistent identifiers), reducing ambiguity and enhancing interoperability across platforms; An open-source data processing application that applies quality control to international standards (SAMOS, or IOOS Qartod); Digital notebooks that manage and capture processing applied to data putting data into context; Democratisation and brokering of data through open data APIs (e.g. ERDDAP, Sensor Web Enablement), allowing end-users to discover and access data, layer their own tools or generate products to meet their own needs; Unambiguous provenance that is maintained throughout the data management workflow using instrument persistent identifiers, part of the latest recommendations by the Research Data Alliance (RDA).  </p> </div><div> <p>Access to universally interoperable oceanic data, with known quality and provenance, will empower a broad range of stakeholder communities, creating opportunities for innovation and impact through data use, re-use and exploitation.</p> </div>


Open Physics ◽  
2012 ◽  
Vol 10 (1) ◽  
Author(s):  
David Nečas ◽  
Petr Klapetek

AbstractIn this article, we review special features of Gwyddion—a modular, multiplatform, open-source software for scanning probe microscopy data processing, which is available at http://gwyddion.net/. We describe its architecture with emphasis on modularity and easy integration of the provided algorithms into other software. Special functionalities, such as data processing from non-rectangular areas, grain and particle analysis, and metrology support are discussed as well. It is shown that on the basis of open-source software development, a fully functional software package can be created that covers the needs of a large part of the scanning probe microscopy user community.


2003 ◽  
Vol 74 (3) ◽  
pp. 1222-1227 ◽  
Author(s):  
Percy Zahl ◽  
Markus Bierkandt ◽  
Stefan Schröder ◽  
Andreas Klust

2016 ◽  
Author(s):  
Brendon O. Watson ◽  
Rafael Yuste ◽  
Adam M. Packer

AbstractWe present an open-source synchronization software package, PackIO, that can record and generate voltage signals to enable complex experimental paradigms across multiple devices. This general purpose package is built on National Instruments data acquisition and generation hardware and has temporal precision up to the limit of the hardware. PackIO acts as a flexibly programmable master clock that can record experimental data (e.g. voltage traces), timing data (e.g. event times such as imaging frame times) while generating stimuli (e.g. voltage waveforms, voltage triggers to drive other devices, etc.). PackIO is particularly useful to record from and synchronize multiple devices, for example when simultaneously acquiring electrophysiology while generating and recording imaging timing data. Experimental control is easily enabled by an intuitive graphical user interface. We also release an open-source data visualisation and analysis tool, EphysViewer, written in MATLAB, as well as a module to import data into Python. These flexible and programmable tools allow experimenters to configure and set up customised input and output protocols in a synchronized fashion for controlling, recording, and analysing experiments.


2015 ◽  
pp. 381-391
Author(s):  
Liguo Yu ◽  
David R. Surma ◽  
Hossein Hakimzadeh

Software development is a fast-changing area. New methods and new technologies emerge all the time. As a result, the education of software engineering is generally considered not to be keeping pace with the development of software engineering in industry. Given the limited resources in academia, it is unrealistic to purchase all the latest software tools for classroom usage. In this chapter, the authors describe how free/open-source data and free/open-source tools are used in an upper-level software engineering class at Indiana University South Bend. Depending on different learning objectives, different free/open-source tools and free/open-source data are incorporated into different team projects. The approach has been applied for two semesters, where instructor's experiences are assembled and analyzed. The study suggests (1) incorporating both free/open-source tools and free/open-source data in a software engineering course so that students can better understand both development methods and development processes and (2) updating software engineering course regularly in order to keep up with the advance of development tools and development methods in industry.


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