scholarly journals The 21st annual Bioinformatics Open Source Conference (BOSC 2020, part of BCC2020)

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1160
Author(s):  
Nomi L. Harris ◽  
Peter J.A. Cock ◽  
Christopher J. Fields ◽  
Karsten Hokamp ◽  
Jessica Maia ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Open Source ◽  
Open Source Software ◽  
Intelligent Systems ◽  
Video Conferencing ◽  
Open Science ◽  
Main Program ◽  
Closed Captioning ◽  
The Galaxy ◽  
Bioinformatics Community

Launched in 2000 and held every year since, the Bioinformatics Open Source Conference (BOSC) is a volunteer-run meeting coordinated by the Open Bioinformatics Foundation (OBF) that covers open source software development and open science in bioinformatics. Most years, BOSC has been part of the Intelligent Systems for Molecular Biology (ISMB) conference, but in 2018, and again in 2020, BOSC partnered with the Galaxy Community Conference (GCC). This year’s combined BOSC + GCC conference was called the Bioinformatics Community Conference (BCC2020, bcc2020.github.io). Originally slated to take place in Toronto, Canada, BCC2020 was moved online due to COVID-19. The meeting started with a wide array of training sessions; continued with a main program of keynote presentations, talks, posters, Birds of a Feather, and more; and ended with four days of collaboration (CoFest). Efforts to make the meeting accessible and inclusive included very low registration fees, talks presented twice a day, and closed captioning for all videos. More than 800 people from 61 countries registered for at least one part of the meeting, which was held mostly in the Remo.co video-conferencing platform.

scholarly journals BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 1054
Author(s):  
Nomi L. Harris ◽  
Peter J. A. Cock ◽  
Christopher J. Fields ◽  
Karsten Hokamp ◽  
Jessica Maia ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Computational Biology ◽  
Open Source ◽  
Open Source Software ◽  
Intelligent Systems ◽  
Open Science ◽  
Global Perspectives ◽  
The Galaxy ◽  
Bioinformatics Community

The 22nd annual Bioinformatics Open Source Conference (BOSC 2021, open-bio.org/events/bosc-2021/) was held online as a track of the 2021 Intelligent Systems for Molecular Biology / European Conference on Computational Biology (ISMB/ECCB) conference. Launched in 2000 and held every year since, BOSC is the premier meeting covering topics related to open source software and open science in bioinformatics. In 2020, BOSC partnered with the Galaxy Community Conference to form the Bioinformatics Community Conference (BCC2020); that was the first BOSC to be held online. This year, BOSC returned to its roots as part of ISMB/ECCB 2021. As in 2020, the Covid-19 pandemic made it impossible to hold the conference in person, so ISMB/ECCB 2021 took place as an online meeting attended by over 2000 people from 79 countries. Nearly 200 people participated in BOSC sessions, which included 27 talks reviewed and selected from submitted abstracts, and three invited keynote talks representing a range of global perspectives on the role of open science and open source in driving research and inclusivity in the biosciences, one of which was presented in French with English subtitles.

scholarly journals BOSC 2019, the 20th annual Bioinformatics Open Source Conference

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 2132
Author(s):  
Nomi L. Harris ◽  
Peter J.A. Cock ◽  
Christopher J. Fields ◽  
Bastian Greshake Tzovaras ◽  
Michael Heuer ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Interest Groups ◽  
Open Source ◽  
Open Source Software ◽  
Intelligent Systems ◽  
Open Science ◽  
Software Documentation ◽  
Training Materials ◽  
Bioinformatics Software ◽  
University Of Cape Town

The Bioinformatics Open Source Conference is a volunteer-organized meeting that covers open source software development and open science in bioinformatics. Launched in 2000, BOSC has been held every year since. BOSC 2019, the 20th annual BOSC, took place as one of the Communities of Special Interest (COSIs) at the Intelligent Systems for Molecular Biology meeting (ISMB/ECCB 2019). The two-day meeting included a total of 46 talks and 55 posters, as well as eight Birds of a Feather interest groups. The keynote speaker was University of Cape Town professor Dr. Nicola Mulder, who spoke on “Building infrastructure for responsible open science in Africa”. Immediately after BOSC 2019, about 50 people participated in the two-day CollaborationFest (CoFest for short), an open and free community-driven event at which participants work together to contribute to bioinformatics software, documentation, training materials, and use cases.

scholarly journals The 2017 Bioinformatics Open Source Conference (BOSC)

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1858
Author(s):  
Nomi L. Harris ◽  
Peter J.A. Cock ◽  
Brad Chapman ◽  
Christopher J. Fields ◽  
Karsten Hokamp ◽  
...  
Keyword(s):  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Open Data ◽  
Open Science ◽  
Research Community ◽  
Biological Research ◽  
Non Profit ◽  
Bioinformatics Software ◽  
Bioinformatics Community

The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC (http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

scholarly journals The 2016 Bioinformatics Open Source Conference (BOSC)

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2464
Author(s):  
Nomi L. Harris ◽  
Peter J.A. Cock ◽  
Brad Chapman ◽  
Christopher J. Fields ◽  
Karsten Hokamp ◽  
...  
Keyword(s):  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Open Science ◽  
Research Community ◽  
Biological Research ◽  
Non Profit ◽  
Link Type ◽  
Bioinformatics Software ◽  
Bioinformatics Community

Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC (http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

scholarly journals Integrated open-source software for multiscale electrophysiology

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Konstantinos Nasiotis ◽  
Martin Cousineau ◽  
François Tadel ◽  
Adrien Peyrache ◽  
Richard M. Leahy ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Analysis Data ◽  
Open Science ◽  
Dense Array ◽  
Unrestricted Access ◽  
Research Transparency ◽  
Programming Skills ◽  
User Friendly

Abstract The methods for electrophysiology in neuroscience have evolved tremendously over the recent years with a growing emphasis on dense-array signal recordings. Such increased complexity and augmented wealth in the volume of data recorded, have not been accompanied by efforts to streamline and facilitate access to processing methods, which too are susceptible to grow in sophistication. Moreover, unsuccessful attempts to reproduce peer-reviewed publications indicate a problem of transparency in science. This growing problem could be tackled by unrestricted access to methods that promote research transparency and data sharing, ensuring the reproducibility of published results. Here, we provide a free, extensive, open-source software that provides data-analysis, data-management and multi-modality integration solutions for invasive neurophysiology. Users can perform their entire analysis through a user-friendly environment without the need of programming skills, in a tractable (logged) way. This work contributes to open-science, analysis standardization, transparency and reproducibility in invasive neurophysiology.

scholarly journals The case for free and open source software in research and scholarship

2021 ◽  
Vol 379 (2197) ◽  
Author(s):  
Laura Fortunato ◽  
Mark Galassi
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Research Process ◽  
Open Science ◽  
Support Staff ◽  
Research Quality ◽  
Open Research ◽  
The Common

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other ‘open’ initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability—including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of ‘open source’ as ‘open code’ is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today. This article is part of the theme issue ‘Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico ’.

scholarly journals Chan Zuckerberg Initiative (CZI) Essential Open Source Software for Science, Cycle 2 Center for Open Science (COS) Proposal - Advancing Sustainability and Innovation of Open Manuscript Services

2020 ◽  
Author(s):  
Kevin Schroeder ◽  
Nicole Pfeiffer ◽  
Brian A. Nosek ◽  
Dasapta Erwin Irawan ◽  
Khaled Moustafa ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Business Models ◽  
Cost Model ◽  
Open Science ◽  
Scholarly Publishing ◽  
Open Model ◽  
New Business ◽  
Open Review ◽  
Peer Community

Preprints (early, complete versions of manuscripts made available online before journal-organized peer review) are shifting the scholarly publishing model by accelerating open access and, potentially, open review. Making these tools interoperable with preprint infrastructure will increase the confidence of the scientific community in preprints. In addition, it will influence commercial publishing services to embrace new business models to innovate towards openness.OSF Preprints is open-source software maintained by the Center for Open Science (COS). OSF Preprints hosts 26 community-run services, providing the ideal conditions to integrate with open review platforms such as Peer Community In (PCI), PREreview, and Hypothes.is and to assess whether a fully open model can compete with and disrupt scholarly publishing across disciplines. We integrated hypothes.is and now propose to add the other platforms.With support from the Alfred P. Sloan Foundation, we are investigating how to improve trust in preprints with signals of credibility to improve chances that an open model can innovate scholarly publishing. Making those signals standard, interoperable, and machine-readable with validation will facilitate adoption and impact. We propose to build open-source open science badges for preprints to be interoperable with other scholarly publishing platforms.In 2020, COS advanced its sustainability plan for the preprints infrastructure with a distributed cost model for the shared infrastructure. Six of the services primarily serve under-resourced scholarly communities in the developing world. We request the costs for maintenance of those services for 2020 to extend their opportunity to develop institutional support for sustaining their services.

scholarly journals OPEN SCIENCE, KNOWLEDGE SHARING AND REPRODUCIBILITY AS DRIVERS FOR THE ADOPTION OF FOSS4G IN ENVIRONMENTAL RESEARCH

2019 ◽  
Vol XLII-4/W14 ◽  
pp. 107-110
Author(s):  
I. Iosifescu Enescu ◽  
G-K. Plattner ◽  
L. Bont ◽  
M. Fraefel ◽  
R. Meile ◽  
...  
Keyword(s):  
Knowledge Sharing ◽  
Open Source ◽  
Open Source Software ◽  
Academic Research ◽  
Open Science ◽  
Environmental Data ◽  
Environmental Research ◽  
Data Repository ◽  
User Requirement ◽  
Data Portal

<p><strong>Abstract.</strong> Support for open science is a highly relevant user requirement for the environmental data portal EnviDat. EnviDat, the institutional data portal and publication data repository of the Swiss Federal Research Institute WSL, actively implements the FAIR (Findability, Accessibility, Interoperability and Reusability) principles and provides a range of services in the area of research data management. Open science, with its requirements for improved knowledge sharing and reproducibility, is driving the adoption of free and open source software for geospatial (FOSS4G) in academic research. Open source software can play a key role in the proper documentation of data sets, processes and methodologies, because it supports the transparency of methods and the precise documentation of all steps needed to achieve the published results. EnviDat actively supports these activities to enhance its support for open science. With EnviDat, WSL contributes to the ongoing cultural evolution in research towards open science and opportunities for distant collaboration.</p>

scholarly journals A brief introduction to Open Data, Open Source Software and Collective Intelligence for environmental data creators and users

2018 ◽  
Author(s):  
Tomislav Hengl ◽  
Ichsani Wheeler ◽  
Robert A MacMillan
Keyword(s):  
Open Access ◽  
Open Source ◽  
Open Source Software ◽  
Collective Intelligence ◽  
Open Data ◽  
Open Science ◽  
Environmental Data ◽  
Key Aspects

Using the term "Open data" has become a bit of a fashion, but using it without clear specifications is misleading i.e. it can be considered just an empty phrase. Probably even worse is the term "Open Science" — can science be NOT open at all? Are we reinventing something that should be obvious from start? This guide tries to clarify some key aspects of Open Data, Open Source Software and Crowdsourcing using examples of projects and business. It aims at helping you understand and appreciate complexity of Open Data, Open Source software and Open Access publications. It was specifically written for producers and users of environmental data, however, the guide will likely be useful to any data producers and user.

The unacknowledged convergence of open source, open access, and open science

First Monday ◽  
2005 ◽  
Author(s):  
John Willinsky
Keyword(s):  
Open Access ◽  
Open Source ◽  
Open Source Software ◽  
Open Science ◽  
Public Access ◽  
Free Software ◽  
Alternative Approach ◽  
Economic Work ◽  
Intellectual Properties ◽  
Reputation Building

A number of open initiatives are actively resisting the extension of intellectual property rights. Among these developments, three prominent instances — open source software, open access to research and scholarship, and open science — share not only a commitment to the unrestricted exchange of information and ideas, but economic principles based on (1) the efficacy of free software and research; (2) the reputation–building afforded by public access and patronage; and, (3) the emergence of a free–or–subscribe access model. Still, with this much in common, the strong sense of convergence among these open initiatives has yet to be fully realized, to the detriment of the larger, common issue. By drawing on David’s (2004; 2003; 2000; 1998) economic work on open science and Weber’s (2004) analysis of open source, this paper seeks to make that convergence all the more apparent, as well as worth pursuing, by those interested in furthering this alternative approach, which would treat intellectual properties as public goods.

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