This document discusses open science and content mining. It begins by defining what "Open" means and why openness is essential. It then discusses topics like open data, content mining scientific literature, and young researchers driving open science forward. Throughout, it emphasizes that the current scholarly publishing system is "broken" and advocates for open as a way to change the system and empower students and researchers. It provides examples of open science heroes and calls students and researchers to action to build an open future together.
This document summarizes a presentation given by Peter Murray-Rust on open science. Some key points from the presentation include:
- Open science and open data are essential for young researchers and students to have the freedom to conduct research and change the world.
- Content mining scientific literature is important but publishers are attempting to control open data and restrict access, which hampers research progress.
- Past student movements have fought for openness and freedom in research, and new approaches may be needed now to change laws and policies to allow content mining while making all research outputs openly available.
Open Data and Open Science presented in Rio for Open Science 2014-08-22. I argue that Open Notebook Science is the way forward and will lead to great benefits
Open access for researchers and students, research managers and publishersIryna Kuchma
The document discusses open access (OA), which refers to free online availability of peer-reviewed literature that allows users to read, download, copy, distribute, print, search, or link to full text articles. It outlines the benefits of OA such as increased citation rates and access, as well as potential cost savings of OA publishing models. Next steps mentioned include encouraging researchers, managers, and libraries to support OA through various policies, repositories, and outreach.
Copyright is one of the greatest barrier to Open Data. This presentation for insidegovernment UK shows the struggle between those who want to reform copyright and those opposed to reform
Keynote talk to LEARN (LERU/H2020 project) for research data management. Emphasizes that problems are cultural not technical. Promotes modern approaches such as Git / continuousIntegration, announces DAT. Asserts that the Right to Read in the Right to Mine. Calls for widespread development of contentmining (TDM)
The Year of Blogging Dangerously: Lessons from the "Blogosphere". This talk will describe how to build an institutional repository using free (or cheap) web-based and blogging tools including flickr.com, slideshare.net, citeulike.org, wordpress.com, myexperiment.org and friendfeed.com. We will discuss some strengths and limitations of these tools and what Institutional Repositories can learn from them.
Bibliography 2.0: A citeulike case study from the Wellcome Trust Genome CampusDuncan Hull
The document discusses Bibliography 2.0, a case study of using the citation management tool Citeulike at the Wellcome Trust Genome Campus. It describes how current publishing incentives encourage "burying" data in publication silos and obscure author identities. Citeulike provides a solution by allowing users to organize citations, see what others are reading, and increase visibility of their work. However, adoption faces barriers from privacy concerns, fragility of tools, and lack of academic rewards for participation.
This document summarizes a presentation given by Peter Murray-Rust on open science. Some key points from the presentation include:
- Open science and open data are essential for young researchers and students to have the freedom to conduct research and change the world.
- Content mining scientific literature is important but publishers are attempting to control open data and restrict access, which hampers research progress.
- Past student movements have fought for openness and freedom in research, and new approaches may be needed now to change laws and policies to allow content mining while making all research outputs openly available.
Open Data and Open Science presented in Rio for Open Science 2014-08-22. I argue that Open Notebook Science is the way forward and will lead to great benefits
Open access for researchers and students, research managers and publishersIryna Kuchma
The document discusses open access (OA), which refers to free online availability of peer-reviewed literature that allows users to read, download, copy, distribute, print, search, or link to full text articles. It outlines the benefits of OA such as increased citation rates and access, as well as potential cost savings of OA publishing models. Next steps mentioned include encouraging researchers, managers, and libraries to support OA through various policies, repositories, and outreach.
Copyright is one of the greatest barrier to Open Data. This presentation for insidegovernment UK shows the struggle between those who want to reform copyright and those opposed to reform
Keynote talk to LEARN (LERU/H2020 project) for research data management. Emphasizes that problems are cultural not technical. Promotes modern approaches such as Git / continuousIntegration, announces DAT. Asserts that the Right to Read in the Right to Mine. Calls for widespread development of contentmining (TDM)
The Year of Blogging Dangerously: Lessons from the "Blogosphere". This talk will describe how to build an institutional repository using free (or cheap) web-based and blogging tools including flickr.com, slideshare.net, citeulike.org, wordpress.com, myexperiment.org and friendfeed.com. We will discuss some strengths and limitations of these tools and what Institutional Repositories can learn from them.
Bibliography 2.0: A citeulike case study from the Wellcome Trust Genome CampusDuncan Hull
The document discusses Bibliography 2.0, a case study of using the citation management tool Citeulike at the Wellcome Trust Genome Campus. It describes how current publishing incentives encourage "burying" data in publication silos and obscure author identities. Citeulike provides a solution by allowing users to organize citations, see what others are reading, and increase visibility of their work. However, adoption faces barriers from privacy concerns, fragility of tools, and lack of academic rewards for participation.
Improving the troubled relationship between Scientists and Wikipedia Duncan Hull
This document discusses improving the relationship between scientists and Wikipedia. It notes that Wikipedia often lacks basic biographical information about notable scientists. A Wikipedian in Residence program was established at the Royal Society to address this issue through edit-a-thons and releasing portraits and data under open licenses. This led to improved coverage of Fellows of the Royal Society on Wikipedia. The document advocates for expanding such programs to other scientific organizations to increase representation of scientists on Wikipedia.
Slides from the "Author Identity – Creating a new kind of reputation online" session at Science Online London (solo09) with Duncan Hull, Geoffrey Bilder, Michael Habib, Reynold Guida
ResearcherID, Contributor ID, Scopus Author ID, etc. help to connect your scientific record. How do these tools connect to your online identity, and how can OpenID and other tools be integrated? How can we build an online reputation and when should we worry about our privacy?
This document summarizes Peter Murray-Rust's speech advocating for open access, open data, and open educational resources. It discusses the history of movements fighting for openness, such as the Free Speech Movement and opposition to SOPA. It highlights individuals and organizations working to make scholarly communications more open and equitable. The speech argues that closed access to research and data hinders progress, and calls the audience to continue efforts to reform publishing practices and build an open scholarly ecosystem through community organizing, software development, and training.
Jean-Claude Bradley was a pioneer of doing Open Science and on 2014-07-14 we held a memorial meeting in Cambridge (see also http://inmemoriamjcb.wikispaces.com/Jean-Claude+Bradley+Memorial+Symposium)
From "Open the Social Sciences" to Open Social ScienceAnkara University
This presentation is from a graduate course, entitled "Open Science," that I taught at "LLM in Intellectual Property" programme of Ankara University in April 2019. For course description, see my personal website at https://ayalcintas.blogspot.com.
This document discusses disruptive communities and technologies in science. It advocates for open access to scientific literature and data to accelerate research. Peter Murray-Rust notes that closed access to publications and data can literally cause harm, as important information is kept from scientists and the public. He promotes the ideas of open access pioneers like Jean-Claude Bradley, who developed open notebook science to openly share the records of research projects. Murray-Rust argues that restricting access to scientific works and data through licensing destroys the ability to freely mine and analyze content, and believes the right to read scientific works should enable open mining of information.
Open access (OA) to scholarly literature recently hit a major milestone: Half of all research articles published become open access, either immediately or after an embargo period. Are the articles you read among them? What about the articles you write? Are the journals to which you submit open-access friendly? What about the journals for which you peer review? Are there any reasons why the public should not have access to the results of taxpayer-funded research?
In this slideshow, Jill Cirasella (Associate Librarian for Public Services and Scholarly Communication, Graduate Center, CUNY) explains the motivation for OA, describes the details of OA, and differentiates between publishing in open access journals (“gold” OA) and self-archiving works in OA repositories (“green” OA). She also dispels persistent myths about OA and examines some of the challenges to OA.
What works and doesn't work in research disseminationtbirdcymru
This document discusses effective strategies for disseminating research findings. It argues that keeping research "closed" is ineffective and that funders now require sharing results as the research progresses. Some effective dissemination strategies mentioned include maintaining a project website, blogging to share work in progress, and using tools like Twitter and SlideShare to engage others. Open access to research is also discussed as increasing impact and affordability. Overall, the document encourages collaborating and sharing research openly and continuously in order to maximize its benefits and influence.
Open Access: What it is and why it is required for scholarly community?Sukhdev Singh
Introduction to Open Access to scholarly literature. Problems with traditional academic publishing and impact of Internet. Definition of Open Access and models. Why Open Access is required for the scientific and scholarly community? What can bloggers do to support Open Access. Open Access status in India.
Talking about Open Access: SMASH and Subtler TacticsJill Cirasella
This document discusses strategies for promoting open access, including forcefully advocating the benefits of open access ("SMASH") or using more subtle tactics. It notes common objections to open access and recommends tailoring the message based on the audience. Open access benefits readers, students, authors, libraries, institutions, and fields of study by increasing access and impact. The document also outlines the progression of open access initiatives at CUNY from 2005 to the present.
Open Access Theses & Dissertations: Airing the Anxieties & Finding the FactsJill Cirasella
Writing a thesis or dissertation is hard, and now that most theses and dissertations are deposited and distributed electronically, graduating students face an additional complication: they must decide whether they want to make their dissertations immediately open access (OA), or, at universities that require OA, they must come to terms with the fact that their work will be OA. In this presentation, I survey and scrutinize the anxieties and myths surrounding OA theses and dissertations.
What the open access movement doesn't want you to knowPattie Pattie
The document discusses issues with the open-access movement that advocates often ignore or downplay. It notes that while open-access aims to provide free access to research, it shifts costs from consumers to authors through article processing fees. This can disadvantage researchers from less-funded institutions. Additionally, the document raises concerns about the exploitative practices and poor quality control of many open-access journals, including fake peer review processes and publishing dubious scientific claims to promote political agendas. The open-access model is seen as prioritizing authors over readers and eliminating value-added services from traditional publishers.
This document provides an overview of open access (OA) publishing and its benefits. It discusses how OA provides free access to scholarly works online, benefiting readers, authors, and fields of study. Both "gold" OA journals that are open from inception, and "green" OA that allows authors to self-archive in repositories, are covered. While traditional publishers claim most readers have access via libraries, the presentation argues that OA benefits many beyond academic institutions as well. Peer review and impact are independent of open access status.
The document provides 17 methods for accessing PDF versions of academic papers and journals, either through the library's subscriptions or other open access options. Some of the key methods mentioned include using the library's Get It button in databases like PubMed, installing browser extensions like Connect and Kopernio that integrate with the library's proxy server, searching hashtags on social media, or as a last resort considering Sci-Hub but noting its illegal status in many countries. The document aims to help readers find legal ways to obtain PDFs through different tools and services.
VOGIN IP 2021 Workshop “Hoe kom ik nu aan de full-text? – Actueler dan ooit, ...Guus van den Brekel
Thuiswerken en off-campus toegang tot wetenschappelijk informatie en bibliotheekdiensten is crucialer dan ooit door Corona. Daarnaast is toegang tot tijdschriften erg prijzig en veel instituten hebben niet de middelen om een licentie op alles te nemen. Vooral organisaties buiten de academische wereld worstelen met toegang tot onderzoek. Bovendien moeten de organisaties met toegang de vraag stellen, wat zullen we doen als we plotseling de toegang tot een reeks tijdschriften verliezen omdat het abonnement is geannuleerd? Als de bibliotheek een artikel niet kan leveren, weten we dat onze gebruikers andere manieren zullen gebruiken om de pdf te krijgen. Echter, deze andere manieren bespreken we bijna nooit. Hoeveel verschillende manieren zijn er precies? Hoe werken ze? Hoe kan ik het groeiende aantal open access-artikelen -die her en der verspreid zijn over het web- op de meest efficiënte manier vinden?
Deelnemers aan de workshop leren over alle mogelijke manieren en hulpmiddelen en krijgen tips om de full-tekst te vinden van wetenschappelijke publicaties. We bespreken “best practices” van bibliotheek-tools en diensten (Linkresolvers, Discovery, LeanLibrary, LibX, Apps, etc.) en testen vooral alle alternatieve tools zoals EndNote Click (voorheen Kopernio), Unpaywall, CORE Discovery, OpenAccess-Button, LibKey Nomad, Google Scholar-Button en andere extensies of bookmarklets.
Your work, your rights? Open access in academia in the Netherlands (2012). Sabine K. Lengger
The document discusses open access (OA) publishing and copyright issues. It notes that OA aims to increase visibility and fairness of research while reducing costs. There are two main types of OA - gold OA journals which are fully open access, and green OA which involves self-archiving in repositories. Many funders now require or encourage OA publishing. While authors often sign over full copyright to journals, they can negotiate to retain some rights like archiving preprints. Students discussed their experiences with OA and suggested hosting workshops and talks to better inform their institution on OA publishing options and copyright issues.
This presentation has basic information about the Rossford Schools Pepsi Refresh Grant for $50,000 -- and we're teaming up with other area schools, too! Learn more and VOTE DAILY! Thank you!!!
Les français et les primaires citoyennes - vague 2contact Elabe
L’intérêt pour les « primaires citoyennes » progresse légèrement auprès des sympathisants de gauche.Le potentiel de participation au premier tour des « primaires citoyennes » se maintient à 5%.Manuel Valls (31%, inchangé) se maintient en tête des souhaits de victoire exprimés par les sympathisants de gauche, devant Benoît Hamon (25%, +1) et Arnaud Montebourg (24%, inchangé).
Improving the troubled relationship between Scientists and Wikipedia Duncan Hull
This document discusses improving the relationship between scientists and Wikipedia. It notes that Wikipedia often lacks basic biographical information about notable scientists. A Wikipedian in Residence program was established at the Royal Society to address this issue through edit-a-thons and releasing portraits and data under open licenses. This led to improved coverage of Fellows of the Royal Society on Wikipedia. The document advocates for expanding such programs to other scientific organizations to increase representation of scientists on Wikipedia.
Slides from the "Author Identity – Creating a new kind of reputation online" session at Science Online London (solo09) with Duncan Hull, Geoffrey Bilder, Michael Habib, Reynold Guida
ResearcherID, Contributor ID, Scopus Author ID, etc. help to connect your scientific record. How do these tools connect to your online identity, and how can OpenID and other tools be integrated? How can we build an online reputation and when should we worry about our privacy?
This document summarizes Peter Murray-Rust's speech advocating for open access, open data, and open educational resources. It discusses the history of movements fighting for openness, such as the Free Speech Movement and opposition to SOPA. It highlights individuals and organizations working to make scholarly communications more open and equitable. The speech argues that closed access to research and data hinders progress, and calls the audience to continue efforts to reform publishing practices and build an open scholarly ecosystem through community organizing, software development, and training.
Jean-Claude Bradley was a pioneer of doing Open Science and on 2014-07-14 we held a memorial meeting in Cambridge (see also http://inmemoriamjcb.wikispaces.com/Jean-Claude+Bradley+Memorial+Symposium)
From "Open the Social Sciences" to Open Social ScienceAnkara University
This presentation is from a graduate course, entitled "Open Science," that I taught at "LLM in Intellectual Property" programme of Ankara University in April 2019. For course description, see my personal website at https://ayalcintas.blogspot.com.
This document discusses disruptive communities and technologies in science. It advocates for open access to scientific literature and data to accelerate research. Peter Murray-Rust notes that closed access to publications and data can literally cause harm, as important information is kept from scientists and the public. He promotes the ideas of open access pioneers like Jean-Claude Bradley, who developed open notebook science to openly share the records of research projects. Murray-Rust argues that restricting access to scientific works and data through licensing destroys the ability to freely mine and analyze content, and believes the right to read scientific works should enable open mining of information.
Open access (OA) to scholarly literature recently hit a major milestone: Half of all research articles published become open access, either immediately or after an embargo period. Are the articles you read among them? What about the articles you write? Are the journals to which you submit open-access friendly? What about the journals for which you peer review? Are there any reasons why the public should not have access to the results of taxpayer-funded research?
In this slideshow, Jill Cirasella (Associate Librarian for Public Services and Scholarly Communication, Graduate Center, CUNY) explains the motivation for OA, describes the details of OA, and differentiates between publishing in open access journals (“gold” OA) and self-archiving works in OA repositories (“green” OA). She also dispels persistent myths about OA and examines some of the challenges to OA.
What works and doesn't work in research disseminationtbirdcymru
This document discusses effective strategies for disseminating research findings. It argues that keeping research "closed" is ineffective and that funders now require sharing results as the research progresses. Some effective dissemination strategies mentioned include maintaining a project website, blogging to share work in progress, and using tools like Twitter and SlideShare to engage others. Open access to research is also discussed as increasing impact and affordability. Overall, the document encourages collaborating and sharing research openly and continuously in order to maximize its benefits and influence.
Open Access: What it is and why it is required for scholarly community?Sukhdev Singh
Introduction to Open Access to scholarly literature. Problems with traditional academic publishing and impact of Internet. Definition of Open Access and models. Why Open Access is required for the scientific and scholarly community? What can bloggers do to support Open Access. Open Access status in India.
Talking about Open Access: SMASH and Subtler TacticsJill Cirasella
This document discusses strategies for promoting open access, including forcefully advocating the benefits of open access ("SMASH") or using more subtle tactics. It notes common objections to open access and recommends tailoring the message based on the audience. Open access benefits readers, students, authors, libraries, institutions, and fields of study by increasing access and impact. The document also outlines the progression of open access initiatives at CUNY from 2005 to the present.
Open Access Theses & Dissertations: Airing the Anxieties & Finding the FactsJill Cirasella
Writing a thesis or dissertation is hard, and now that most theses and dissertations are deposited and distributed electronically, graduating students face an additional complication: they must decide whether they want to make their dissertations immediately open access (OA), or, at universities that require OA, they must come to terms with the fact that their work will be OA. In this presentation, I survey and scrutinize the anxieties and myths surrounding OA theses and dissertations.
What the open access movement doesn't want you to knowPattie Pattie
The document discusses issues with the open-access movement that advocates often ignore or downplay. It notes that while open-access aims to provide free access to research, it shifts costs from consumers to authors through article processing fees. This can disadvantage researchers from less-funded institutions. Additionally, the document raises concerns about the exploitative practices and poor quality control of many open-access journals, including fake peer review processes and publishing dubious scientific claims to promote political agendas. The open-access model is seen as prioritizing authors over readers and eliminating value-added services from traditional publishers.
This document provides an overview of open access (OA) publishing and its benefits. It discusses how OA provides free access to scholarly works online, benefiting readers, authors, and fields of study. Both "gold" OA journals that are open from inception, and "green" OA that allows authors to self-archive in repositories, are covered. While traditional publishers claim most readers have access via libraries, the presentation argues that OA benefits many beyond academic institutions as well. Peer review and impact are independent of open access status.
The document provides 17 methods for accessing PDF versions of academic papers and journals, either through the library's subscriptions or other open access options. Some of the key methods mentioned include using the library's Get It button in databases like PubMed, installing browser extensions like Connect and Kopernio that integrate with the library's proxy server, searching hashtags on social media, or as a last resort considering Sci-Hub but noting its illegal status in many countries. The document aims to help readers find legal ways to obtain PDFs through different tools and services.
VOGIN IP 2021 Workshop “Hoe kom ik nu aan de full-text? – Actueler dan ooit, ...Guus van den Brekel
Thuiswerken en off-campus toegang tot wetenschappelijk informatie en bibliotheekdiensten is crucialer dan ooit door Corona. Daarnaast is toegang tot tijdschriften erg prijzig en veel instituten hebben niet de middelen om een licentie op alles te nemen. Vooral organisaties buiten de academische wereld worstelen met toegang tot onderzoek. Bovendien moeten de organisaties met toegang de vraag stellen, wat zullen we doen als we plotseling de toegang tot een reeks tijdschriften verliezen omdat het abonnement is geannuleerd? Als de bibliotheek een artikel niet kan leveren, weten we dat onze gebruikers andere manieren zullen gebruiken om de pdf te krijgen. Echter, deze andere manieren bespreken we bijna nooit. Hoeveel verschillende manieren zijn er precies? Hoe werken ze? Hoe kan ik het groeiende aantal open access-artikelen -die her en der verspreid zijn over het web- op de meest efficiënte manier vinden?
Deelnemers aan de workshop leren over alle mogelijke manieren en hulpmiddelen en krijgen tips om de full-tekst te vinden van wetenschappelijke publicaties. We bespreken “best practices” van bibliotheek-tools en diensten (Linkresolvers, Discovery, LeanLibrary, LibX, Apps, etc.) en testen vooral alle alternatieve tools zoals EndNote Click (voorheen Kopernio), Unpaywall, CORE Discovery, OpenAccess-Button, LibKey Nomad, Google Scholar-Button en andere extensies of bookmarklets.
Your work, your rights? Open access in academia in the Netherlands (2012). Sabine K. Lengger
The document discusses open access (OA) publishing and copyright issues. It notes that OA aims to increase visibility and fairness of research while reducing costs. There are two main types of OA - gold OA journals which are fully open access, and green OA which involves self-archiving in repositories. Many funders now require or encourage OA publishing. While authors often sign over full copyright to journals, they can negotiate to retain some rights like archiving preprints. Students discussed their experiences with OA and suggested hosting workshops and talks to better inform their institution on OA publishing options and copyright issues.
This presentation has basic information about the Rossford Schools Pepsi Refresh Grant for $50,000 -- and we're teaming up with other area schools, too! Learn more and VOTE DAILY! Thank you!!!
Les français et les primaires citoyennes - vague 2contact Elabe
L’intérêt pour les « primaires citoyennes » progresse légèrement auprès des sympathisants de gauche.Le potentiel de participation au premier tour des « primaires citoyennes » se maintient à 5%.Manuel Valls (31%, inchangé) se maintient en tête des souhaits de victoire exprimés par les sympathisants de gauche, devant Benoît Hamon (25%, +1) et Arnaud Montebourg (24%, inchangé).
The document provides an evaluation of a graphic narrative project. The author summarizes how their final product followed their original intentions from the storyboard, with some changes that improved the work. While the beginning followed the flat plans closely, more relevant details from the plans were included as the book went on. The layout also changed from multiple images per page to one image per page for better aesthetics. In conclusion, the original intentions were generally followed and changes made improvements.
The Salvation Army provides social services and assistance to those in need. Their mission is based on the Bible and motivated by the love of God. They help through programs like adult rehabilitation, elderly services, children's programs, disaster relief and operating thrift stores. Funds raised through donations and thrift store sales go back into the community through services like food assistance, homeless shelters and substance abuse treatment.
This three day online training program provides facilitator skills training. Penny Valentine will serve as the instructor over the asynchronous course. The training will cover establishing an online presence, communication skills, learning theories, and tools for online teaching. Trainees will participate in discussions, assignments, and a final assessment. The goal is to help new online facilitators develop the skills needed to manage an online classroom and engage distance learners.
This 3-page resume provides details about Md. Mominur Rahman's education, skills, and experience. He is currently a 4th semester student studying Electrical Electronic Engineering at Daffodil International University. Previously, he completed a Diploma in Electro-Medical Technology from Brahmanbaria Polytechnic Institute in 2015. His computer skills include Microsoft Office applications and experience with Windows operating systems. He is proficient in English and Bengali. Personal details are also provided such as date of birth, address, marital status, and references.
RxJS permite o uso de Observáveis que emitem valores assíncronos ao longo do tempo de forma reativa. Observáveis podem ser mapeados, filtrados e compostos usando operadores funcionais de forma similar a Iteráveis, porém lidando também com assincronicidade e múltiplos valores.
The document discusses future trends in instructional settings and modalities, focusing on open learning and mobile learning by the year 2026. Open learning gives learners flexibility in choosing what, when, where, and how they learn. Mobile learning occurs via mobile devices and allows learning anytime, anywhere. These trends are driven by users, institutions, instructors, businesses, and technology developers. Academic and professional environments will embrace these trends to meet learner and worker needs. Learners, institutions, instructors, businesses, and technology designers will facilitate developing and designing adult education. Instructional design will focus on learning spaces and better opportunities for learners.
The document outlines the key phases and elements of an effective communication plan for organizational change:
1) The four phases of a communication plan include pre-change approval, creating need for change, midstream change communication, and confirming/celebrating change success.
2) Technology like text, social media, email can be used to communicate the plan. Feedback should include both metrics and qualitative comments.
3) Managing negativity involves recognizing contributions, opportunities, clear expectations, and fair treatment. Evaluating impact examines the success of the final phase of confirming and celebrating change.
This document is a resume for Johannes Arend van Hensbergen, who has a PhD in Industrial Chemistry from the University of New South Wales. He has over 3 years of work experience in various industries including chemicals, adhesives, consumer products, food, beverages, and coatings. He also has strong project management, problem solving, and communication skills developed through his research and work experiences.
Presentation given at NUI, Galway 2019-04-11 for Open Science Week.
An overview of Early Career Researchers, their innovation and contribution towards Open Infrastructure
Published on Jan 29, 2016 by PMR
Keynote talk to LEARN (LERU/H2020 project) for research data management. Emphasizes that problems are cultural not technical. Promotes modern approaches such as Git / continuous Integration, announces DAT. Asserts that the Right to Read in the Right to Mine. Calls for widespread development of content mining (TDM)
The Culture of Research Data, by Peter Murray-RustLEARN Project
1st LEARN Workshop. Embedding Research Data as part of the research cycle. 29 Jan 2016. Presentation by Peter Murray-Rust, ContentMine.org and University of Cambridge
Early Career Reseachers in Science. Start Early, Be Open , Be Bravepetermurrayrust
Highlights the importance of supporting Early Career Researchers to pursue their own ideas, possibly alongside their main research. Illustrated with biology but applies to all fields of science. This was a 14 min presentation and shows narratives of how ECRs develop and reinforce each other.
Published on Nov 26, 2014 by PMR
Followup meeting in London to OpenCon2014, on the need for different models of scholarly communication. I explore the history of 20thC academic student-based revolutions, with special relevance to young people and the scope for action today.
The Publisher -Academic complex is a dystopian cycle where academia gives (mega)publishers manuscripts, reviews and money and the publishers give personal and institutional glory(vanity). This is analysed in its origins, impact and harm. The disruption can come from Advocacy/Activism, Community and Tools. Disruption comes from doing things Better or Novel, not Prices
AUDIO : https://soundcloud.com/damahub/peter-murray-rust-disturbing-the-publisher-academic-complex-210418-british-library
Thanks to DaMaHub
This has now been edited by Ewan McAndrew (Edinburgh Wikimedian in Residence) many thanks - to synchronize the slides with the soundtrack. https://media.ed.ac.uk/media/1_46h85ltt Brilliant
Publishing your research: Open Access (introduction & overview)Jamie Bisset
Open Access: what is it and what do I need to do? (November 2013) slides. Delivered as part of the Durham University Researcher Development Programme. Further Training available at https://www.dur.ac.uk/library/research/training/
Amanuens.is HUmans and machines annotating scholarly literaturepetermurrayrust
about 10,000 scholarly articles ("papers") are published each day. Amanuens.is is a symbiont of ContentMine and Hypothes.is (both Shuttleworth projects/Fellows) which annotates theses using an array of controlled vocabularies ("dictionaries"). The results, in semantic form are used to annotate the original material. The talk had live demos and used plant chemistry as the examples
Amanuens.is HUmans and machines annotating scholarly literature TheContentMine
Published on May 19, 2016 by PMR
about 10,000 scholarly articles ("papers") are published each day. Amanuens.is is a symbiont of ContentMine and Hypothes.is (both Shuttleworth projects/Fellows) which annotates theses using an array of controlled vocabularies ("dictionaries"). The results, in semantic form are used to annotate the original material. The talk had live demos and used plant chemistry as the examples
ContentMining for France and Europe; Lessons from 2 years in UKpetermurrayrust
This document summarizes Peter Murray-Rust's presentation on two years of content mining in the UK and lessons for France and Europe. Some key points discussed include:
- Content mining can save lives by enabling researchers to search literature and find past warnings, as in the case of Ebola.
- However, publishers like Elsevier and Wiley have stopped researchers' content mining efforts, hampering their work.
- France, Europe and the UK must actively support content mining through funding, tools, training and protecting researchers from restrictive publishers.
- Examples are given of ContentMine fellows' projects mining literature on topics like weevil-plant associations, cell migration and depression in animals.
This document provides a summary of a presentation on open scientific knowledge and building a knowledgebase beyond traditional journals. The presentation discusses the problems with publishers controlling infrastructure and restricting access to knowledge. It demonstrates software tools like getpapers and AMI that can be used to freely access and search across scientific literature. The presentation advocates for open access to all scientific literature and building a sustainable community and organization to achieve this goal.
Automatic Extraction of Science and Medicine from the scholarly literatureTheContentMine
Published on Jun 04, 2015 by PMR
Many scientists have to extract many facts out the scholarly literature - to evaluate other work or to extract useful collections of facts. This shows the approach, especially for systematic reviews of animal or clinical trials
Automatic Extraction of Science and Medicine from the scholarly literaturepetermurrayrust
Many scientists have to extract many facts out the scholarly literature - to evaluate other work or to extract useful collections of facts. This shows the approach, especially for systematic reviews of animal or clinical trials
Digital Scholarship: Enlightenment or Devastated Landscape? TheContentMine
Published on Dec 17, 2015 by PMR
Every year 500 Billion USD of public funding is spent on research, but much of this lies hidden in papers that are never read. I describe how machines can help us to read the literature. However there is massive opposition from publishers who are trying to prevent open scholarship and who build walled gardens that they control
Every year 500 Billion USD of public funding is spent on research, but much of this lies hidden in papers that are never read. I describe how machines can help us to read the literature. However there is massive opposition from publishers who are trying to prevent open scholarship and who build walled gardens that they control
Young people in an Age of Knowledge Neocolonialismpetermurrayrust
Peter Murray-Rust presents on the topic of neocolonialism in knowledge and scholarly publishing. He argues that megacorporations currently control knowledge infrastructure through closed access publishing models, which increases inequality between rich and poor scholars. This parallels Kwame Nkrumah's description of neocolonialism, where foreign capital is used to exploit rather than develop less developed parts of the world. Murray-Rust advocates for building an open knowledgebase controlled by researchers rather than corporations to give young people and less developed scholars more opportunity to participate and change the world. He supports this through advocacy, community building, and open tools and technologies like ContentMine that can extract and analyze knowledge from literature.
Published on Jul 10, 2015 by PMR
Scholarly Publishing wastes huge amounts of valuable science. This presentation to the Public Library of Science suggests how we can work together to put this right
Scholarly Publishing wastes huge amounts of valuable science. This presentation to the Public Library of Science suggests how we can work together to put this right
English Essay Narrative Techniques. Online assignment writing service.Jill Swenson
The document provides instructions for requesting writing assistance from HelpWriting.net in 5 steps:
1. Create an account with a password and email.
2. Complete a 10-minute order form with instructions, sources, and deadline.
3. Choose a writer based on their bid, qualifications, history, and feedback.
4. Review the paper and authorize payment or request revisions.
5. Request revisions to ensure satisfaction and receive a refund if plagiarized.
Paradise Lost and The Right to Read is the Right to Minepetermurrayrust
Presented to UIUC CIRSS seminars to a mixed group of Library, CS, domain scientists with a great contingent of Early Career Researchers. Starts by honouring the creation of the wonderful NCSA Mosaic at UIUC in 1993 and the paradise of knowledge and community it opened. Then shows the gradual and tragic decline of the web into a megacorporate neocolonialist empire, where knowledge is sacrificed for money and power.
You have seen many of the slides before but the words are different and have been recorded.
Similar to Principles and practice of Open Science (20)
High throughput mining of the scholarly literature TheContentMine
Published on Jun 7, 2016 by PMR
Talk given to statisticians in Tilburg, with emphasis on scholarly comms for detecting unusual features. Includes demo of Amanuens.is and image mining
This document summarizes Peter Murray-Rust's presentation on open content and programs at MIOSS 2016. It discusses how open approaches can lead to faster, better, and more inclusive research. It provides examples of open source tools for tasks like chemical entity recognition, structure identification, and chemical language parsing. It also describes efforts to openly mine scientific literature to extract facts and analyze large amounts of data.
Automatic Extraction of Knowledge from the LiteratureTheContentMine
Published on May 11, 2016 by PMR
ContentMine tools (and the Harvest alliance) can be used to search the literature for knowledge, especially in biomedicine. All tools are Open and shortly we shall be indexing the complete daily scholarly literature
Automatic Extraction of Knowledge from Biomedical literature TheContentMine
Published on Mar 16, 2016 by PMR
A plenary lecture to Cochrane Collaboration in Birmingham, on the value of automatically extracting knowledge. Covers the Why? How? What? Who? and problems and invites collaboration
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Published on Mar 4, 2016 by PMR
Text and data mining (TDM) techniques can be applied to a wide range of materials, from published research papers, books and theses, to cultural heritage materials, digitised collections, administrative and management reports and documentation, etc. Use cases include academic research, resource discovery and business intelligence.
This workshop will show the value and benefits of TDM techniques and demonstrate how ContentMine aims to liberate 100,000,000 facts from the scientific literature, and ContentMine will provide a hands on demo on a topical and accessible scientific/medical subject.
Published on Feb 29, 2016 by PMR
An overview of Text and Data Mining (ContentMining) including live demonstrations. The fundamentals: discover, scrape, normalize , facet/index, analyze, publish are exemplified using the recent Zika outbreak. Mining covers textual and non-textual content and examples of chemistry and phylogenetic tress are given.
Published on Feb 07, 2016 by PMR
Use of ContentMine tools on the Open Access subset of EuropePubMedCentral to discover new knowledge about the Zika virus. Includes clips of the software in action
This document summarizes Peter Murray-Rust's work on mining scientific images and extracting structured information from them. It discusses his software tools for image analysis, including recognizing figures, tables, chemical structures, phylogenetic trees and extracting data. It provides examples of extracting information from images and transforming unstructured data in PDFs into semantic, computable formats. The document also discusses opportunities for collaboration and making the software openly available.
Open Knowledge and University of Cambridge European Bioinformatics InstituteTheContentMine
This document discusses open data and open science. It highlights Jean-Claude Bradley as a pioneer of open notebook science and open data who believed closed data means people die. It describes tools like ContentMine that can automatically extract data like chemical reactions, phylogenetic trees and clinical trial results from papers. Visitors can extract specific types of data while repositories can solve problems communally with continuous publication and validation.
Can Computers understand the scientific literature (includes compscie material)TheContentMine
Published on Jan 24, 2014 by PMR
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Jean-Claude Bradley's vision of open notebook science aims to change how science is done by making all research processes and outputs openly accessible in real-time. This addresses significant waste in the current system where most research funds are wasted due to flawed design, non-publication and poor reporting of results. Open science is inspired by open source software which engineers repositories for transparent and collaborative development, validation and improvement by global communities. The combination of openness, truth and community can optimize scientific processes and outputs.
Published on Jul 24, 2014 by PMR
PhD Theses are normally locked away digitally. They cost 20 billion dollars to create and we waste much of this value. By making them open we can use software to read, index, reuse, compute and add massive value
Published on Aug 22, 2014 by PMR
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Published on Nov 13, 2014 by PMR
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The talk , delivered to the Computational Institute, will be /was followed by a hands-on workshop learning how to use the technology and work as a community.
Published on Mar 05, 2015 by PMR
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Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
Principles and practice of Open Science
1. Open Science
Peter Murray-Rust,
ContentMine.org, and University of Cambridge
Opencon2015, Bologna, IT 2015-11-18
What is “Open”?
Why is it essential?
Open Data
Content Mining – a battle we must win
Young researchers are the present (Mike Eisen)
2. The Right to Read is the Right to Mine**PeterMurray-Rust, 2011
http://contentmine.org
4. Messages
• The system is completely broken
• We are at war with major publishers
• Students have the power to change the world
• Universities need help from students
• Open is a state of mind
• The opposite of Open is broken [1]
• Friction destroys Open
• Don’t buy it, build it …
• … TOGETHER
[1] (John Wilbanks)
5. @Senficon (Julia Reda) :Text & Data mining in times of
#copyright maximalism:
"Elsevier stopped me doing my research"
http://onsnetwork.org/chartgerink/2015/11/16/elsevi
er-stopped-me-doing-my-research/ … #opencon #TDM
Breaking news:
Elsevier stopped me doing my research
Chris Hartgerink
6. I am a statistician interested in detecting potentially problematic research such as data fabrication,
which results in unreliable findings and can harm policy-making, confound funding decisions, and
hampers research progress.
To this end, I am content mining results reported in the psychology literature. Content mining the
literature is a valuable avenue of investigating research questions with innovative methods. For
example, our research group has written an automated program to mine research papers for errors in
the reported results and found that 1/8 papers (of 30,000) contains at least one result that could
directly influence the substantive conclusion [1].
In new research, I am trying to extract test results, figures, tables, and other information reported in
papers throughout the majority of the psychology literature. As such, I need the research papers
published in psychology that I can mine for these data. To this end, I started ‘bulk’ downloading research
papers from, for instance, Sciencedirect. I was doing this for scholarly purposes and took into account
potential server load by limiting the amount of papers I downloaded per minute to 9. I had no intention
to redistribute the downloaded materials, had legal access to them because my university pays a
subscription, and I only wanted to extract facts from these papers.
Full disclosure, I downloaded approximately 30GB of data from Sciencedirect in approximately 10 days.
This boils down to a server load of 0.0021GB/[min], 0.125GB/h, 3GB/day.
Approximately two weeks after I started downloading psychology research papers, Elsevier notified
my university that this was a violation of the access contract, that this could be considered stealing of
content, and that they wanted it to stop. My librarian explicitly instructed me to stop downloading
(which I did immediately), otherwise Elsevier would cut all access to Sciencedirect for my university.
I am now not able to mine a substantial part of the literature, and because of this Elsevier is directly
hampering me in my research.
[1] Nuijten, M. B., Hartgerink, C. H. J., van Assen, M. A. L. M., Epskamp, S., & Wicherts, J. M. (2015). The
prevalence of statistical reporting errors in psychology (1985–2013). Behavior Research Methods, 1–22.
doi: 10.3758/s13428-015-0664-2
Chris Hartgerink’s blog post
8. Open Content Mining of FACTs
Machines can interpret chemical reactions
We have done 500,000 patents. There are >
3,000,000 reactions/year. Added value > 1B Eur.
9. C) What’s the problem with this spectrum?
Org. Lett., 2011, 13 (15), pp 4084–4087
Original thanks to ChemBark
12. catalogue
getpapers
query
Daily
Crawl
EuPMC, arXiv
CORE , HAL,
(UNIV repos)
ToC
services
PDF HTML
DOC ePUB
TeX XML
PNG
EPS CSV
XLSURLs
DOIs
crawl
quickscrape
norma
Normalizer
Structurer
Semantic
Tagger
Text
Data
Figures
ami
UNIV
Repos
search
Lookup
CONTENT
MINING
Chem
Phylo
Trials
Crystal
Plants
COMMUNITY
plugins
Visualization
and Analysis
PloSONE, BMC,
peerJ… Nature, IEEE,
Elsevier…
Publisher Sites
scrapers
queries
taggers
abstract
methods
references
Captioned
Figures
Fig. 1
HTML tables
30, 000 pages/day
Semantic ScholarlyHTML
Facts
CONTENTMINE Complete OPEN Platform for Mining Scientific Literature
13. Stand back! I am about to do
ContentMining!
• Erriquez Daniela, Esame finale: Bologna, Aprile 2014
• Dott.ssa Elena Fiorentini, n. 0000274966, TESI DI DOTTORATO, Bologna
• Qian Gou, Esame finale: Bologna, finale 2014
• Maurizio BARONTINI, UNIVERSITÀ DEGLI STUDI DELLA TUSCIA DI VITERBO
• Terracciano Mario, Esame finale anno 2014
15. Copyright and Mining
• UK (“Hargreaves”) 2014 legislation:
– “personal” “non-commercial*” “research” “data
analytics”
– legitimizes copying (?to disk), but not publishing
• PMR-premise: You cannot do reproducible
scientific mining and avoid violating copyright.
19. http://www.nytimes.com/2015/04/08/opinion/yes-we-were-warned-about-
ebola.html
We were stunned recently when we stumbled across an article by European
researchers in Annals of Virology [1982]: “The results seem to indicate that
Liberia has to be included in the Ebola virus endemic zone.” In the future,
the authors asserted, “medical personnel in Liberian health centers should be
aware of the possibility that they may come across active cases and thus be
prepared to avoid nosocomial epidemics,” referring to hospital-acquired
infection.
Adage in public health: “The road to inaction is paved with research
papers.”
Bernice Dahn (chief medical officer of Liberia’s Ministry of Health)
Vera Mussah (director of county health services)
Cameron Nutt (Ebola response adviser to Partners in Health)
A System Failure of Scholarly Publishing
20. [1] The Military-Industrial-Academic complex (1961)
(Dwight D Eisenhower, US President)
Publishers Academia
Glory+?
$$, MS
review
Taxpayer
Student
Researcher
$$ $$
in-kind
The Publisher-Academic complex[1]
21. [Wikipedia:] On the steps of Sproul Hall [Student] Mario Savio gave a
famous speech
... But we're a bunch of raw materials that don't mean … to end up being
bought by some clients of the University, be they the government, be they
industry, be they organized labor, be they anyone! We're human beings!
... There's a time when the operation of the machine becomes so odious
— makes you so sick at heart — that you can't take part. You can't even
passively take part. And you've got to put your bodies upon the gears and
upon the wheels, upon the levers, upon all the apparatus, and you've got
to make it stop. And you've got to indicate to the people who run it, to the
people who own it, that unless you're free, the machine will be prevented
from working at all. [1]
Univ California,
Berkeley 1964
The Free Speech Movement
22. 1970’s UK,
student occupations and sit-ins
University of Stirling
Used without permission but with thanks and Love
Liverpool , Warwick, Emmanuel Coll Camb., UCL, Glasgow, Middlesex, …
24. ["How We Stopped SOPA”:
This bill ... shut down whole websites. Essentially, it stopped Americans from
communicating entirely with certain groups....
I called all my friends, and we stayed up all night setting up a website for this new group,
Demand Progress, with an online petition opposing this noxious bill.... We [got] ... 300,000
signers.... We met with the staff of members of Congress and pleaded with them.... And then
it passed unanimously....
And then, suddenly, the process stopped. Senator Ron Wyden ... put a hold on the
bill.[48][49]
He added, "We won this fight because everyone made themselves the hero of their own
story. Everyone took it as their job to save this crucial freedom.”
Robert Swartz: "Aaron was killed by the government, and MIT betrayed all of its basic
principles."[116]
Aaron Swartz
25. Rules for Revolutionaries
• Be publicly clear about your public aims.
• Gather whole-hearted allies.
• Choose your moment/s carefully.
• Be prominent – blogs, talks, papers.
• Be bold – and probably brave.
• Write Liberation Software.
• Create slogans, warcries, mantras.
26. Take the fight to publishers. Hold them accountable for the near-
criminal business models they operate on, and the stranglehold they
have had on academia for too long.
Extending this, I need your help. I want to know if we initiate a formal
investigation into the practices of publishers, in terms of the fact that
they operate within an unregulated market and enjoy enormous
profits to commit immoral acts (creating knowledge inequality). …. I
want to know what we can do, and if such an investigation is even
feasible, and whether or not we have a legal case supporting us.
Don’t sacrifice your career.. [PMR] said it best, that for any revolution
blood will be spilled. If you’re making someone angry, you’re probably
doing it right. But when you’re ‘advocating’ for open access, maintain
one simple rule: don’t be a dick…. (and lots more)
Jon Tennant 2014-11-25
http://blogs.egu.eu/palaeoblog/2014/11/25/open-access-wins-all-of-
the-arguments-all-of-the-time/
27. The Right to Read
is
The Right to Roam
The Right to Mine
Kinder Mass Trespass
used without permission but with love and thanks
28. How can we achieve Freedom?
• Change the law to allow ContentMining
– Hard, tedious, but necessary
– Requires evidence, campaigning, making yourselves a
pain in the arse…
• Make all outputs Open
– Requires culture change in researchers
– Tools: Open Notebook Science, Github, Open source,
Social media.
– Needs support from funders, learned societies,
universities
29. Four Freedoms (Richard Stallman)
The freedom to:
0 run the program as you wish, for any purpose
1 study how the program works, and change it
2 to redistribute copies
3 distribute copies of your modified program
Most other “Opens” follow these principles, including CC-BY material.
However “Green Open Access” is incompatible with Freedom2 and 3
30. The Open Definition
“Open means anyone can freely access, use, modify, and share for
any purpose (subject, at most, to requirements that preserve
provenance and openness).”
31. http://www.budapestopenaccessinitiative.org/read
… an unprecedented public good. …
… completely free and unrestricted access to [peer-
reviewed literature] by all scientists, scholars, teachers,
students, and other curious minds. …
…Removing access barriers to this literature will
accelerate research, enrich education, share the
learning of the rich with the poor and the poor with
the rich, make this literature as useful as it can be, and
lay the foundation for uniting humanity in a common
intellectual conversation and quest for knowledge.
(Budapest Open Access Initiative, 2003)
32. Panton Principles for Open Data in
science(2010)
• PUBLISH YOUR DATA OPENLY
• …make an explicit and robust statement of your wishes.
• Use a recognized waiver or license that is appropriate for
data.
• open as defined by the Open Knowledge/Data Definition
(… NOT non-commercial)
• Explicit dedication of data … into the public domain via
PDDL or CCZero
Peter Murray-Rust, Cameron Neylon, Rufus Pollock, John
Wilbanks
34. Bjorn Brembs enhanced by OpenData
http://bjoern.brembs.net/2015/11/dont-be-afraid-of-open-data/
This is a response to Dorothy Bishop’s post “Who’s afraid of open data?“.
After we had published a paper on how Drosophila strains that are referred to by the same name in the literature
(Canton S), but came from different laboratories behaved completely different in a particular behavioral experiment,
Casey Bergman from Manchester contacted me, asking if we shouldn’t sequence the genomes of these five fly strains
to find out how they differ. So I went and behaviorally tested each of the strains again, extracted the DNA from the 100
individuals I had just tested and sent the material to him. I also published the behavioral data immediately on our
GitHub project page.
Casey then sequenced the strains and made the sequences available, as well. A few weeks later, both Casey and I
were contacted by Nelson Lau at Brandeis, showing us his bioinformatics analyses of our genome data. Importantly,
his analyses wasn’t even close to what we had planned. On the contrary, he had looked at something I (not being a
bioinformatician) would have considered orthogonal (Casey may disagree). So there we had a large chunk of work we
would have never done on the data we hadn’t even started analyzing, yet. I was so thrilled! I learned so much from
Nelson’s work, this was fantastic! Nelson even asked us to be co-author, to which I quickly protested and suggested, if
anything, I might be mentioned in the acknowledgments for “technical assistance” – after all, I had only extracted the
DNA.
However, after some back-and-forth, he persuaded me with the argument that he
wanted to have us as co-authors to set an example. He wanted to show everyone that
sharing data is something that can bring you direct rewards in publications. He
wanted us to be co-authors as a reward for posting our data and as incentive for
others to let go of their fears and also post their data online.
35. Arguments for Open
• Open Science:
– is Better Science
– can reach and involve everyone
– Open Science moves more quickly
– Open Science challenges injustice
– helps the world
It also happens to:
– Promote the careers of scientists
– Save money
36. Jean-Claude Bradley
Jean-Claude Bradley was one of the
most influential open scientists of our
time. He was an innovator in all that
he did, from Open Education to
bleeding edge Open Science; in 2006,
he coined the phrase Open Notebook
Science. His loss is felt deeply by
friends and colleagues around the
world.
On Monday July 14, 2014 we shall
gather at Cambridge University to
honour his memory and the legacy he
leaves behind with a highly
distinguished set of invited speakers to
revisit and build upon the ideas which
inspired and defined his life’s work.
Wikipedia CC BY-SA
37. Traditional Research and Publication
“Lab” work paper/th
esis
Write
rewrite
Re-experiment
publish
???
Validation??
DATA
output “belongs”
to publisher
process “belongs”
to publisher
Walls of
academia
52. Young people
Jenny Molloy
Ross Mounce
Sam Moore Peter Kraker Rosie GraySophie Kay
Sophie: 3rd yr Grad students train 1st year students
PANTON ARMS
Panton Fellows
54. Rotation-Based Learning (RBL)
Phase 1: Initiator
• No communication
permitted between groups
• Attempt to reproduce
existing literature
• Deliver a coherent research
story by the end of Phase 1
Phase 2: Successor
• Communication between
groups still prohibited
• Validate and develop the
inherited research story
• Critique your predecessors
• Role of research producer vs. research user
• Can this approach help to foster awareness of reproducibility issues?
Throughout Phases 1 & 2:
• Daily lectures on open
science culture & techniques
• First-hand application to own
research work
• Version control using GitHub
• Daily group supervision
55. “Do you think you would be
more confident in the future
about trying to apply Open
techniques to your work..?”
• 50% Yes, by myself
• 41% Yes, with help/guidance
• 9% No opinion/neutral
• 0% No
56. Some Children
of the Digital Enlightenment
• David Carroll & Joe McArthur: OAButton
• Rayna Stamboliyska & Pierre-Carl Langlais
• Jon Tennant
• Ross Mounce
• Jenny Molloy
• Erin McKiernan
• Jack Andraka
• Michelle Brook
• Heather Piwowar
• TheContentMine Team
• Rufus Pollock
• Jonathan Gray
• Sophie Kay
Jean-Claude Bradley [1] a chemist
developed Open notebook science;
making the entire primary record of a
research project publicly available
online as it is recorded. (WP)
J-C promoted these ideas with
UNDERGRADUATE scientists.
[1] Unfortunately J-C died in 2014;
we held a memorial meeting in
Cambridge
Sophie
Kay
57. More Thoughts
• Don’t negotiate with walled gardens, make
them change or make them obsolete
• Building on top of non-Open is very fragile,
unpredictable and usually bad engineering
58. Protecting innovation
• Many start-ups get acquired and lose their
mission
• “Embrace, extend, exterminate” (Microsoft)
• Consider adding “Open Lock” clauses to
articles of incorporation
Editor's Notes
Hi, I’m here to talk about AMI; a data extraction framework and tool. First, I just want highlight some of key contributors to the projects; Andy for his work on the ChemistryVisitor and Peter for the overall architecture.
In this talk, I’m going to impress the importance of data in a specific format and its utility to automated machine processing. Then I’m going to demonstrate AMI’s architecture and the transformation of data as it flows through the process. I’m going to dwell a little on a core format used, Scalable Vector Graphics (SVG) before introducing the concept of visitors, which are pluggable context specific data extractors. Next, I’m going to introduce Andy’s ChemVisitor, for extracting semantic chemistry data, along with a few other visitors that can process non-chemistry specific data. Finally, I will demonstrate some uses of the ChemVisitor, within the realm of validation and metabolism.