Galaxy Training: A powerful framework for teaching! | PLOS Computational Biology

Abstract:  There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.

 

 

Yes, Scholar-Publishers Can Make Common Cause After All | Allegra Lab

by Anne Brackenbury Last spring, I began work with the open access advocacy group, Libraria, as a Community Convener to help organize a mutual aid network amongst a group of open access publications in anthropology and adjacent fields. Cooperate for Open (or C4O, as this network is affectionately known), is motivated by the idea that there is a wide variety of open access models suitable for different contexts and scales. In the case of C4O the focus is on small, scholar-led, open access publications that consistently find themselves — sometimes deliberately — on the margins of scholarly publishing. I wrote a piece for Allegra Lab about the rationale behind the project when I began this contract, wondering whether (and hoping that) scholar-publishers could make common cause. Now, as my work winds down, it seems as good a time as any to offer my answer to that question. […]  

Introducing the Open Book Collective (OBC) | Jun 8, 2022 | YouTube

“Open Book Collective is a non-profit that connects academics, librarians, publishers, and service providers to collectively sustain the infrastructures, relationships, and organizations vital for the success of open access book publishing. Through the Open Book Collective platform, publishers and publishing service providers can offer research institutions the option to financially support their work through library membership programs. Librarians can access the platform to explore and assess different initiatives, support Open Access collections, and manage their subscriptions. OBC’s legal and governance structure ensures it can’t be co-opted for profit, and that stakeholders have a meaningful say in its future. We provide financial support to new open access initiatives and connect book publishers to sustainable revenue streams. Open Book Collective is helping build a world where open access books are produced and distributed collaboratively and anti-competitively, without technical or economic barriers. …”

Publizieren in der Medienwissenschaft — Andreas Kirchner über Open Access als Standard | Open Media Studies

by Andreas Kirchner

englisch version via gTranslate:

I recently noticed that the editors of the journal MEDIENwissenschaft: Reviews | Reviews has started to specifically mark Open Access publications that are subject to review – a clear indication of a change in media studies publication practice. In book list 4/22, 64 out of 186 titles, a third of all publications listed there, bear the new “OA” abbreviation. This is not a bad rate, especially considering that the open access transformation of books has only picked up speed in recent years. The spectrum of the 19 publishers that published the books is enormous: imprints from the multinational publishing groups SpringerNature and Taylor & Francis are represented as well as various university presses or small scientific and non-fiction publishers such as Büchner or Frank & Timme. The Bielefelder transcript-Verlag occupies a special position, which in recent years has been particularly committed to establishing Open Access in German-language media studies: 17 OA books on the “Book List” have been published there alone. In this illustrious circle, the name of a publishing house can be found – and that at least four times -meson press .

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Next Generation Library Project Makes Progress Toward Shared Open Publishing Infrastructure – SPARC

“The Next Generation Library Publishing (NGLP) project is working to change that by providing libraries with resources to create a robust, values-driven, and community-led system to share knowledge. With support from an Arcadia Fund grant, the NGLP began as a collaboration of Strategies for Open Science (Stratos), the California Digital Library (CDL), and Educopia with three co-investigators: Kristen Ratan, Catherine Mitchell and Katherine Skinner.

The team gathered feedback from the library community, developed open-source software, and has piloted technology solutions that are showing promising results. Their aim is to provide tools that will help librarians become key players as publishers –  complementing their work as repository managers – to offer a sustainable, non-commercial alternative as knowledge brokers….

One pilot included five library publishers interested in testing a turnkey, hosted journal and institutional repository solution. Another, led by California Digital Library (CDL), tested the NGLP ecosystem’s ability to serve a large consortial publisher hosting in-house. And yet another, led by University of North Carolina Press and Longleaf Services, tested a journal and journal portal solution. All participants are eager to continue production services. …”

CfP Special Issue of Teknokultura: Emergence of critical experimental practices in publishing and digital posthumanities | Teknokultura. Revista de Cultura Digital y Movimientos Sociales

As open access policies have become assimilated to the commercial dynamics of academic knowledge production and circulation, publishing processes in the academic setting have emerged as strategic spaces where to explore new styles of research and social intervention, as well as to transform the relationship between academia and political activism amidst the globalization and digitalization of capitalism. The anthology Whose Book is it Anyway? Views from Elsewhere on Publishing, Copyright, and Creativity, edited by Janis Jefferies and Sarah Kember (Open Book Publishers, 2020), problematizes the technicism and commercial orientation of mainstream discourses on open access that pervade most governments and higher education institutions. The authors call on us to think beyond technological ‘progress’ and copyright issues, and to focus for once on moral, political and social rights as well as concrete strategies for academic-led editorial practices driven not by profit, but by solidarity, critique, and creativity. From this feminist intersectional perspective, developed in the After Open Access Manifesto, the issue is no longer to be for or against copyright, or even open access, but to inaugurate and sustain new types of research and a more just future for academic publications within and beyond discourses of digitisation. This special issue calls on contributions that document and reflect on the emergence of critical experimental practices in publishing and digital posthumanities which have a feminist orientation and commitment to intervene in political and cultural debates on open access and open science. The goal is to map emergent discourses and practices on academic-led publishing across geographies and languages, including interpretations and controversies on open access and open science in different contexts as well as cultural critiques of instrumentalist understandings of technology and intellectual work in academic settings, all paying particular attention to feminist approaches to the problem of knowledges in the current crisis of globalization. Topics include but are not limited to:

Intersectional feminism and open access/open science debates in specific contexts
Editorial activisms in the digital sphere
Experimental, iterative and processual publishing led in academic settings
Feminist ethics in academic-led publishing
Platforms and knowledge economies
Geopolitics of academic knowledge
Socioenvironmental dimensions of academic publishing

Manuscripts should be submitted by September 15, 2023. They can be submitted in Spanish, English or Portuguese, must be original and not have been previously published or under consideration by other journals or publications.

 

OpenCon Librarian Community Call | November 08, 2022 | Daniel Goodman

“…On Tuesday, November 8th, Daniel Goodman, one of several authors of the “Open letter to the WHOSTP and Subcommittee on Open Science” join the OpenCon Librarian Community call to discuss the motivations, goals, and experiences of the Open letter. He will also share his future vision for academic publishing through the recently launched Neuromatch Open Publishing initiative. Neuromatch proposes an open publishing platform owned by the community on which work would be free to read and publish, and all data would be made freely and openly available for third parties to build additional services on….”

Library Publishing Coalition: Annual Report 2021-2022

“While scholarly publishing is a core function of academia, the commercial companies that have traditionally controlled a majority of publications often hold values that run counter to those of the faculty whose work they publish. This includes the publication of content behind paywalls, which ties breadth of dissemination to profits. In efforts to better serve their parent institutions, faculty, and the common good, libraries began establishing publishing programs that support the publication needs and efforts of their institution while maximizing access to publications. While each library publishing program differs in its structure, goals, and focus, these programs build on the skills of librarians in scholarship, metadata, and publishing, and align with the values of their institutions, often prioritizing open access, open source software, and new and emerging publication types. This scaffolding and expertise ensure that those producing the scholarship have increased control over the production, publication, and ownership of their publications….”

Why is managing open access so painful?

“Over the last decade or so, there has been a steady transition in scholarly publishing away from a traditional subscription based revenue model for publishers towards open access models where published articles are freely available to readers1 . During the early part of the transition, author-pays models, where a researcher finds money to pay article processing charges (APCs), were shown to be sustainable under certain conditions by publishers like BioMed Central and PLOS and grew in popularity among commercial publishers2 . In more recent years, concerns about rising APCs and lack of access to publication funds in many disciplines, coupled with funder mandates3 aimed at accelerating transitions to openness, have led to a number of new business models, from so-called ‘diamond’ open access4 where publication costs are covered by a third-party fund, to transformative agreements, such as ‘read and publish’ aimed at enabling journals to move from subscription to open access models with institutional support5 . Alongside all of these sits ‘green OA’, in which authors self-archive a version of their article in a suitable disciplinary or institutional repository while the published version appears in a subscription-based journal. This increasingly complex landscape poses a problem for universities as they find themselves administering a diverse range of open access agreements. At the same time, very little research has been done into how universities deal with open access. Anecdotally, approaches to OA funding are varied and sometimes ad hoc. In general, it appears that university libraries often distribute information to researchers and scholars about sources of open access funding, but no clear picture exists of how funds are allocated or monitored. With this in mind, in late 2021, we launched a community survey, supported by MoreBrains Cooperative6 , about the current state of the open access landscape7 . With 64 responses from 22 countries, although this is a relatively small sample, several themes emerge strongly, some of which we had already intuited, and some that were more surprising….

Half (32) of all respondents reported low levels of trust in the management of OA publishing and associated charges compared to 39% (25) who reported that they neither trusted nor distrusted the status quo and just 11% (7) who reported moderate or high levels of trust. There was strong support for open APC data (43), open standards for data exchange (41) and clear institutional ownership of data (42), with about 65% of all respondents claiming that each of those measures would increase trust. Seven of the eight free text responses also mentioned transparency and improved reporting as being desirable. Although no single measure emerged as a clear first priority, these ideas share a common theme of greater coordination and coherence across the many stakeholders involved in OA. In a similar vein, community governance structures for OA data were favoured by over half (34) of all respondents….” 

Removing author fees can help open access journals make research available to everyone

“Publishing a journal requires money, but that amounts to only 10 to 15 per cent of what publishers charge authors to make their work open access. Author fees are disproportionate with publishing costs, and correlate to the journal’s prestige, impact and profit model.

In this environment, author fees will continue to increase so long as someone can pay for it. It also means that open access publishing privileges a certain set of researchers….”

From Mattering Press to the Open Book Collective: Interview with Joe Deville | Community-led Open Publication Infrastructures for Monographs (COPIM)

Corazza, F., & Fathallah, J. (2022). From Mattering Press to the Open Book Collective: Interview with Joe Deville. Community-Led Open Publication Infrastructures for Monographs (COPIM). https://doi.org/10.21428/785a6451.ffebd406

As well as being the Chair of the Open Book Collective, due to launch soon, Joe Deville is one of the founders of Mattering Press, a small Open Access book publisher. We sat down with Joe to speak to him about how he became involved in Open Access publishing, some of the challenges that small publishers can face when starting up, and how his work with Mattering Press led to his involvement in the Open Book Collective.

 

NEW COMMUNITIES: SCHOLAR-LED PUBLISHING UND OPEN ACCESS — Aktuelle scholar-led Publishing-Initiativen und Open Access in den Geistes- und Sozialwissenschaften (Teil 3) | Open Media Studies

by Tobias Steiner

 

«[M]ight it not be helpful to think of open access less as a project and model to be implemented, and more as a process of continuous struggle and critical Resistance?» (Adema and Hall, 2013)

«[I]f we are theorists, if we are radical, critical theorists, then our critique should aim at a transformation of the actual systems within which we work.» (Joy, 2017)

via deepl.com

In the first part of this blog series, scholar-led publishing was classified and situated in the context of Open Access. In the second part, I worked diachronically – with a focus on journals – how scholar-led initiatives from the field of cultural and media studies created their own spaces in the digital realm at an early stage and, through these, realized their respective individual interpretations of the basic motivation that also underlies Open Access: enabling free access to knowledge. In the third part, I will present a selection of scholar-led book publishers relevant to cultural and media studies, as well as collaborations, networks, and infrastructure initiatives.

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OLD TRADITIONS: SCHOLAR-LED PUBLISHING UND OPEN ACCESS — zu den Anfängen digitalen scholar-led Publishings in den Geistes- und Sozialwissenschaften (Teil 2) | Open Media Studies

by Tobias Steiner

«Apparently, there are academics, and reputable ones at that, for whom the cost/benefit of the Mercedes Benz — the smart cover, prestigious logo, beautiful paper, and added-value galore — is less important than the means of quick and effective conveyance, even if it be merely a rusty old heap that runs. Academic aspirations are, in many cases, being modified by the financial realities of the day. I believe this is leading us to a more differentiated array of publications. I imagine the Internet full of curiously painted VW beetles and vans, an engaging mixture of information vehicles. If this speculation becomes reality, and if our academics and their institutions become aware that the current style of single-minded high-value publishing can lead to perishing, then we are headed for some value shifts over time.»

Anna Shumelda Okerson: Oh Lord, Won’t You Buy Me A Mercedes Benz Or, There is a There There, in: Surfaces, Bd. IV, Nr. 102, 1994, Folio 1.

via deepl.com

For the humanities and social sciences, early scholar-led publishing projects and initiatives that emerged and experimented with the new digital medium, especially before the widespread history of OA cited in the first part, still play a role that is too little noticed in the broad sense. As Moore, for example, points out with reference to early digital journal initiatives, numerous scholar-led initiatives from the humanities and social sciences existed well before the early 2000s, which are generally regarded as the start of the OA movement. These initiatives – also as a reaction to the strong commercialization of the journal market in the 1970s and 1980s2 – had set themselves the goal of organizing the production and circulation of scholarly communication in the digital realm themselves and making it freely accessible to the public.

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PLURALITIES: SCHOLAR-LED PUBLISHING UND OPEN ACCESS — zur Rolle von scholar-led publishing in den Geistes- und Sozialwissenschaften (Teil 1) | Open Media Studies

by Tobias Steiner

Publikationskulturen sind im Wissenschaftsbetrieb ähnlich vielfältig wie die ihnen zugrundeliegenden Forschungskulturen. Im heutzutage oftmals normativ geführten Diskurs um Open Access besteht die Gefahr, dass diese Vielfalt zugunsten techno-solutionistischer Implementationen ins Hintertreffen gerät oder gar mittelfristig verloren geht. Im Folgenden möchte ich daher näher auf den Ansatz des scholar-led publishing eingehen und aufzeigen, welche Zusammenhänge zwischen scholar-led Initiativen und der ‹klassischen› Open Access-Bewegung bestehen.

Dazu beginne ich mit einer kurzen Diskurseinordnung und leite dann diachron ab, wie scholar-led Initiativen aus den Geistes- und Sozialwissenschaften – und mit ihnen aus den Kultur-, Medien- und Kommunikationswissenschaften – schon früh und parallel zu den weithin rezipierten Entwicklungen aus dem medizinisch-naturwissenschaftlichen Bereich der 1990er Jahre auf eigene Weise wichtige Impulse zur Öffnung von Publikationskulturen setzten. Im zweiten Teil stelle ich dazu ein Spektrum von scholar-led Journal-Initiativen vor, während der dritte Teil sich scholar-led Buchverlagen sowie scholar-led Netzwerken im weiteren Sinn zuwendet.

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