The document discusses open science and open access. It provides examples of open science like open access publishing, open notebooks, prepublication data release, and open source software. It discusses three aspects of open science: cost, restrictions, and timing. It discusses the costs of publishing, creative commons licenses, and examples of organizations that promote open access like the Public Library of Science (PLoS) and how they circulated an open letter to encourage open access. Overall, the document discusses the history and concepts of open science and open access.
Jonathan Eisen talk on "Open Science" at #BOSC2012 #ISMBJonathan Eisen
This document summarizes a talk on open science given by Jonathan Eisen. Some key points:
1. Eisen recounted his early skepticism of open access but eventual conversion after experiences like publishing an open access paper that received more attention.
2. He discussed experiments with openly releasing genomic data that helped convince him of the benefits of openness in science.
3. Eisen argued that limiting access to scientific literature and data hinders scientific progress, and outlined several ways scientists can promote openness.
Can machines understand the scientific literature?petermurrayrust
This document summarizes a presentation on machines understanding scientific literature. It discusses using content mining to address global challenges like climate change and epidemics. It presents work using semantic markup, Wikidata, image analysis and other tools to extract structured information from text and images to help researchers. Challenges from publishers limiting text and data mining are also discussed.
The document discusses open science and open access. It provides examples of open science like open access publishing, open notebooks, prepublication data release, and open source software. It discusses three aspects of open science: cost, restrictions, and timing. It discusses the costs of publishing, creative commons licenses, and examples of organizations that promote open access like the Public Library of Science (PLoS) and how they circulated an open letter to encourage open access. Overall, the document discusses the history and concepts of open science and open access.
Jonathan Eisen talk on "Open Science" at #BOSC2012 #ISMBJonathan Eisen
This document summarizes a talk on open science given by Jonathan Eisen. Some key points:
1. Eisen recounted his early skepticism of open access but eventual conversion after experiences like publishing an open access paper that received more attention.
2. He discussed experiments with openly releasing genomic data that helped convince him of the benefits of openness in science.
3. Eisen argued that limiting access to scientific literature and data hinders scientific progress, and outlined several ways scientists can promote openness.
Can machines understand the scientific literature?petermurrayrust
This document summarizes a presentation on machines understanding scientific literature. It discusses using content mining to address global challenges like climate change and epidemics. It presents work using semantic markup, Wikidata, image analysis and other tools to extract structured information from text and images to help researchers. Challenges from publishers limiting text and data mining are also discussed.
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
Semantic content created from Open Access papers to help in the fight against viral epidemics. Includes contributions from NIPGR interns, 5 supported by Indian National Young Academy of Scientists.
This document discusses two upcoming events from OpenVirus and CEVOpen focusing on plant science literature. Part 1 will have a group of young Indian scientists discussing how to mine scholarly literature to find hidden science. Part 2 will be a fun game designed by Gita Yadav's research group to have non-science colleagues collect and analyze papers on plants, countries, and chemicals from a database of 200,000 open articles. The game aims to educate while being collaborative or competitive. The document also provides context on the organizer's previous work developing literature mining tools and collaborations on plant science research.
The University of Notre Dame College of Science welcomed two new faculty members in fall 2013:
1) Luqun Shen joined the Department of Biological Sciences as an assistant professor. His research focuses on understanding how cells sense and respond to environmental stresses using budding yeast as a model organism.
2) John Kwon joined the Department of Chemistry and Biochemistry as an assistant professor. His research group uses mass spectrometry-based proteomics to study post-translational modifications and their roles in human disease.
Automatic Extraction of Knowledge from the Literaturepetermurrayrust
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
Opening up to Diversity talk by @phylogenomics at #UCDPHSAJonathan Eisen
This document summarizes the key points of an article on the diversity and composition of bacteria in indoor environments. It finds that the bacterial communities found indoors are less diverse than outdoors, and that mechanically ventilated rooms contain less diverse communities than window ventilated rooms. Certain building attributes like ventilation source, airflow rates, humidity and temperature are correlated with the diversity and types of bacteria present. Rooms with lower airflow and humidity have higher abundances of potential human pathogens. The study suggests that building design and operation can manage the indoor microbiome and species that may colonize the human microbiome.
Opening up Scientific and Scholarly CommunicationJonathan Eisen
The document discusses the history and goals of the Public Library of Science (PLoS), an organization founded in 2000 to promote open access scientific publishing. PLoS circulated an open letter calling for freely accessible scientific literature and launched their own open access journals, PLoS Biology and PLoS Medicine, after not enough publishers supported open access. The document also describes the author's personal experience with lack of access to scientific papers delaying treatment for his stillborn son, which reinforced his views that limiting access is unethical and counterproductive to advancing scientific knowledge.
This document summarizes a talk on open science given by Jonathan Eisen. Some key points:
1. Eisen recounted his early skepticism of open access but eventual conversion after experiences like publishing an open access paper that received more attention.
2. He discussed experiments with openly releasing genomic data that helped convince him of the benefits of openness in science.
3. Eisen argued that limiting access to scientific literature and data hinders scientific progress, and outlined several ways scientists can promote openness.
This document summarizes the history and evolution of open access scientific publishing, focusing on the role of the Public Library of Science (PLoS). It discusses how PLoS pioneered open access publishing through petitions and journals in 2001. It then covers how PLoS helped establish PubMed Central and advocated for policies like the NIH public access policy. The document outlines PLoS's current experiments with metrics, commenting tools, and other innovations to improve access and reuse of research.
PLOS (Public Library of Science) is a nonprofit open-access publisher founded in 2001 with a mission to accelerate scientific progress. PLOS makes research articles immediately and freely available worldwide under open-access licenses. It publishes several peer-reviewed journals covering various scientific fields like biology, medicine, and genetics. PLOS advocates for openness in science through open data sharing, transparent peer review processes, and making research outputs openly accessible for all.
This document provides instructions for unlocking an eBook. It directs the user to visit a website to redeem a code, type in the code, click redeem, and log in or sign up. It states that accessing the eBook is easy and allows browsing content online or offline on any device through a mobile app. It provides contact information for technical assistance.
Genetic engineering involves copying and rearranging parts of living things to create new organisms from non-living parts. It has potential benefits like cures for diseases and altered foods, but also risks like allergic reactions to engineered foods and ethical issues. Leaders in the field mentioned include Craig Venter, Art Caplan, Daniel Sulsmay, Lawrence Goldstein, and George Daley. As a bio chemist, Ben Mosca studies disease-causing organisms and tests drugs, and has experience in biotechnology academies and studying chemistry in college. He also volunteers in his community.
Workshop finding and accessing data - fiona - lunteren april 18 2016Fiona Nielsen
Workshop presentation on finding and accessing human genomics data for research.
Including statistics of publicly available data sources and tips on how to save time in your workflow of data access.
Presented at BioSB2016, pre-conference PhD retreat for young researchers in bioinformatics and systems biology at Congrescentrum De Werelt in Lunteren. #BioSB2016 #BioSB16
Link to event:
http://www.youngcb.nl/events/biosb-phd-retreat-2016/
Read more about my work:
http://DNAdigest.org
http://repositive.io
https://uk.linkedin.com/in/fionanielsen
1. The document discusses issues around transparency and communication with research participants in biobanks and clinical trials.
2. Cases are presented where researchers were reluctant to share basic information or results with participants.
3. The author argues that dedicated resources and a culture shift towards more transparency are needed to better inform and engage participants about how their data and samples are being used in research.
This presentation was provided by John Inglis of Cold Spring Harbor Laboratory during the NISO virtual conference, The Preprint: Integrating the Form into the Scholarly Ecosystem, held on February 14, 2018.
The document summarizes a proposal for Tinnitusbook, an online community for tinnitus researchers. It describes similar existing communities like the Alzheimer Research Forum and Stembook.org. Tinnitusbook would connect researchers and patients to facilitate collaboration and rapid progress in tinnitus research. It would provide resources like publications, annotations, discussions, and links to genes/proteins. Existing software and experience creating other communities could help establish Tinnitusbook.
Presentation given at Open Science question and answer session hosted by the Institute for Quantitative Social Science (IQSS), and the Office for Scholarly Communication (OSC) at Harvard University, on July 16th 2014.
Free and open access, transparent assessment and dissemination of research in a fast, shared, collaborative, participative and clear manner for all of society are some of the principles of Open Science. The recognition and adoption of open research practices is growing, including new policies that increase public access to scholarly literature and encourage openness of codes and data sharing for its reproduction. Among these initiatives which are reconfiguring scientific communication, preprints have been consolidating themselves as a promising space for free, open and transparent knowledge, streamlining the editorial process. Preprints are the first formal step in making the manuscripts publicly available before being approved by a journal.
The logics of publishing based on science guiding principles have always been in the decision-making power of the editor. From the choice of referees to the distribution of articles approved in publishing editions, the time management to publish keeping quality, periodicity and celerity regarding feedback on the output was always a challenge to editors. Moreover, this time management becomes an even greater challenge to the publishing process in Brazil, and in some parts of Latin America, whose journals’ management is mainly based on voluntary work. Given this scenario, initiatives that seek to make scientific communication faster and more transparent appear as solutions to the daily difficulties of scientific publishing, such as, for instance, preprints, continuous publication and open peer review.
In view of this new reconfiguration of the editorial process, this panel aims to discuss the panorama of fast and transparent scientific communication, seeking to share experiences that have been developed that respond to the editorial demands on the management of time and quality of the papers published in scientific journals and, particularly, to support the development of the SciELO Program preprints policy.
Syllabus
The challenges of scientific publishing and editorial ethics regarding time management and quality; initiatives for fast research communication; metrics and alternative indicators of scientific visibility; preprints and continuous communication experience in the national and international scenario; editorial dynamics of preprints and its models in the market; the demands of the continuous publication flow; open modalities of peer review: peer-review, open peer-review, and crowd-based peer review; the spaces of fast communication in scholarly social platforms.
From the event "Specimen Science: Ethics and Policy Implications," held at Harvard Law School on November 16, 2015.
This event was a collaboration between The Center for Child Health and Policy at Case Western Reserve University and University Hospitals Rainbow Babies & Children’s Hospital; the Petrie-Flom Center for Health Law Policy, Biotechnology, and Bioethics at Harvard Law School; the Multi-Regional Clinical Trials Center of Harvard and Brigham and Women's Hospital; and Harvard Catalyst | The Harvard Clinical and Translational Science Center. It was supported by funding from the National Human Genome Research Institute and the Oswald DeN. Cammann Fund at Harvard University.
For more information, visit our website at http://petrieflom.law.harvard.edu/events/details/specimen-science-ethics-and-policy
This document provides an overview of key concepts from Chapter 1 of a biology textbook. It begins by defining what science is and the scientific method. It describes early experiments that disproved spontaneous generation and established the principle that all life comes from pre-existing life. It then characterizes the basic properties of living things, including being made of cells, reproducing, responding to stimuli, and evolving over time. Finally, it introduces tools used in biology like microscopes and techniques like cell culture and fractionation. The goal is to introduce foundational topics in the science of biology.
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
Semantic content created from Open Access papers to help in the fight against viral epidemics. Includes contributions from NIPGR interns, 5 supported by Indian National Young Academy of Scientists.
This document discusses two upcoming events from OpenVirus and CEVOpen focusing on plant science literature. Part 1 will have a group of young Indian scientists discussing how to mine scholarly literature to find hidden science. Part 2 will be a fun game designed by Gita Yadav's research group to have non-science colleagues collect and analyze papers on plants, countries, and chemicals from a database of 200,000 open articles. The game aims to educate while being collaborative or competitive. The document also provides context on the organizer's previous work developing literature mining tools and collaborations on plant science research.
The University of Notre Dame College of Science welcomed two new faculty members in fall 2013:
1) Luqun Shen joined the Department of Biological Sciences as an assistant professor. His research focuses on understanding how cells sense and respond to environmental stresses using budding yeast as a model organism.
2) John Kwon joined the Department of Chemistry and Biochemistry as an assistant professor. His research group uses mass spectrometry-based proteomics to study post-translational modifications and their roles in human disease.
Automatic Extraction of Knowledge from the Literaturepetermurrayrust
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
Opening up to Diversity talk by @phylogenomics at #UCDPHSAJonathan Eisen
This document summarizes the key points of an article on the diversity and composition of bacteria in indoor environments. It finds that the bacterial communities found indoors are less diverse than outdoors, and that mechanically ventilated rooms contain less diverse communities than window ventilated rooms. Certain building attributes like ventilation source, airflow rates, humidity and temperature are correlated with the diversity and types of bacteria present. Rooms with lower airflow and humidity have higher abundances of potential human pathogens. The study suggests that building design and operation can manage the indoor microbiome and species that may colonize the human microbiome.
Opening up Scientific and Scholarly CommunicationJonathan Eisen
The document discusses the history and goals of the Public Library of Science (PLoS), an organization founded in 2000 to promote open access scientific publishing. PLoS circulated an open letter calling for freely accessible scientific literature and launched their own open access journals, PLoS Biology and PLoS Medicine, after not enough publishers supported open access. The document also describes the author's personal experience with lack of access to scientific papers delaying treatment for his stillborn son, which reinforced his views that limiting access is unethical and counterproductive to advancing scientific knowledge.
This document summarizes a talk on open science given by Jonathan Eisen. Some key points:
1. Eisen recounted his early skepticism of open access but eventual conversion after experiences like publishing an open access paper that received more attention.
2. He discussed experiments with openly releasing genomic data that helped convince him of the benefits of openness in science.
3. Eisen argued that limiting access to scientific literature and data hinders scientific progress, and outlined several ways scientists can promote openness.
This document summarizes the history and evolution of open access scientific publishing, focusing on the role of the Public Library of Science (PLoS). It discusses how PLoS pioneered open access publishing through petitions and journals in 2001. It then covers how PLoS helped establish PubMed Central and advocated for policies like the NIH public access policy. The document outlines PLoS's current experiments with metrics, commenting tools, and other innovations to improve access and reuse of research.
PLOS (Public Library of Science) is a nonprofit open-access publisher founded in 2001 with a mission to accelerate scientific progress. PLOS makes research articles immediately and freely available worldwide under open-access licenses. It publishes several peer-reviewed journals covering various scientific fields like biology, medicine, and genetics. PLOS advocates for openness in science through open data sharing, transparent peer review processes, and making research outputs openly accessible for all.
This document provides instructions for unlocking an eBook. It directs the user to visit a website to redeem a code, type in the code, click redeem, and log in or sign up. It states that accessing the eBook is easy and allows browsing content online or offline on any device through a mobile app. It provides contact information for technical assistance.
Genetic engineering involves copying and rearranging parts of living things to create new organisms from non-living parts. It has potential benefits like cures for diseases and altered foods, but also risks like allergic reactions to engineered foods and ethical issues. Leaders in the field mentioned include Craig Venter, Art Caplan, Daniel Sulsmay, Lawrence Goldstein, and George Daley. As a bio chemist, Ben Mosca studies disease-causing organisms and tests drugs, and has experience in biotechnology academies and studying chemistry in college. He also volunteers in his community.
Workshop finding and accessing data - fiona - lunteren april 18 2016Fiona Nielsen
Workshop presentation on finding and accessing human genomics data for research.
Including statistics of publicly available data sources and tips on how to save time in your workflow of data access.
Presented at BioSB2016, pre-conference PhD retreat for young researchers in bioinformatics and systems biology at Congrescentrum De Werelt in Lunteren. #BioSB2016 #BioSB16
Link to event:
http://www.youngcb.nl/events/biosb-phd-retreat-2016/
Read more about my work:
http://DNAdigest.org
http://repositive.io
https://uk.linkedin.com/in/fionanielsen
1. The document discusses issues around transparency and communication with research participants in biobanks and clinical trials.
2. Cases are presented where researchers were reluctant to share basic information or results with participants.
3. The author argues that dedicated resources and a culture shift towards more transparency are needed to better inform and engage participants about how their data and samples are being used in research.
This presentation was provided by John Inglis of Cold Spring Harbor Laboratory during the NISO virtual conference, The Preprint: Integrating the Form into the Scholarly Ecosystem, held on February 14, 2018.
The document summarizes a proposal for Tinnitusbook, an online community for tinnitus researchers. It describes similar existing communities like the Alzheimer Research Forum and Stembook.org. Tinnitusbook would connect researchers and patients to facilitate collaboration and rapid progress in tinnitus research. It would provide resources like publications, annotations, discussions, and links to genes/proteins. Existing software and experience creating other communities could help establish Tinnitusbook.
Presentation given at Open Science question and answer session hosted by the Institute for Quantitative Social Science (IQSS), and the Office for Scholarly Communication (OSC) at Harvard University, on July 16th 2014.
Free and open access, transparent assessment and dissemination of research in a fast, shared, collaborative, participative and clear manner for all of society are some of the principles of Open Science. The recognition and adoption of open research practices is growing, including new policies that increase public access to scholarly literature and encourage openness of codes and data sharing for its reproduction. Among these initiatives which are reconfiguring scientific communication, preprints have been consolidating themselves as a promising space for free, open and transparent knowledge, streamlining the editorial process. Preprints are the first formal step in making the manuscripts publicly available before being approved by a journal.
The logics of publishing based on science guiding principles have always been in the decision-making power of the editor. From the choice of referees to the distribution of articles approved in publishing editions, the time management to publish keeping quality, periodicity and celerity regarding feedback on the output was always a challenge to editors. Moreover, this time management becomes an even greater challenge to the publishing process in Brazil, and in some parts of Latin America, whose journals’ management is mainly based on voluntary work. Given this scenario, initiatives that seek to make scientific communication faster and more transparent appear as solutions to the daily difficulties of scientific publishing, such as, for instance, preprints, continuous publication and open peer review.
In view of this new reconfiguration of the editorial process, this panel aims to discuss the panorama of fast and transparent scientific communication, seeking to share experiences that have been developed that respond to the editorial demands on the management of time and quality of the papers published in scientific journals and, particularly, to support the development of the SciELO Program preprints policy.
Syllabus
The challenges of scientific publishing and editorial ethics regarding time management and quality; initiatives for fast research communication; metrics and alternative indicators of scientific visibility; preprints and continuous communication experience in the national and international scenario; editorial dynamics of preprints and its models in the market; the demands of the continuous publication flow; open modalities of peer review: peer-review, open peer-review, and crowd-based peer review; the spaces of fast communication in scholarly social platforms.
From the event "Specimen Science: Ethics and Policy Implications," held at Harvard Law School on November 16, 2015.
This event was a collaboration between The Center for Child Health and Policy at Case Western Reserve University and University Hospitals Rainbow Babies & Children’s Hospital; the Petrie-Flom Center for Health Law Policy, Biotechnology, and Bioethics at Harvard Law School; the Multi-Regional Clinical Trials Center of Harvard and Brigham and Women's Hospital; and Harvard Catalyst | The Harvard Clinical and Translational Science Center. It was supported by funding from the National Human Genome Research Institute and the Oswald DeN. Cammann Fund at Harvard University.
For more information, visit our website at http://petrieflom.law.harvard.edu/events/details/specimen-science-ethics-and-policy
This document provides an overview of key concepts from Chapter 1 of a biology textbook. It begins by defining what science is and the scientific method. It describes early experiments that disproved spontaneous generation and established the principle that all life comes from pre-existing life. It then characterizes the basic properties of living things, including being made of cells, reproducing, responding to stimuli, and evolving over time. Finally, it introduces tools used in biology like microscopes and techniques like cell culture and fractionation. The goal is to introduce foundational topics in the science of biology.
OMICS Publishing Group, Journal of Hereditary Genetics, is an international, peer-reviewed journal publishing original research articles helpful to understand the general concept of heritability. The Hereditary Genetics under Open Access Category is a focus of current development in the areas of Heredity and Genetics.
Data science sig june 23, 2017 introduction, comments and feedbackData Science NIH
This document provides an overview of a webinar titled "Global Perspective on Biobanking and Access to Samples" that took place on June 23, 2017. The webinar featured presentations from experts in biobanking from the United States, Netherlands, Spain, Australia, and other countries. They discussed topics such as finding and accessing biospecimen data internationally, rare disease samples, academic biorepository operations, and improving biospecimen consent processes. Attendees provided positive feedback and questions on incentivizing sharing of rare disease samples and data, locating rare disease specimens, and collaborating with patient groups.
This document provides an overview of a webinar titled "Global Perspective on Biobanking and Access to Samples" that took place on June 23, 2017. The webinar featured presentations from experts in biobanking from the United States, Netherlands, Spain, Australia, and other countries. They discussed topics such as finding and accessing rare disease samples, academic biorepository operations, sample locators, and issues specific to rare disease biobanks. Attendees provided positive feedback and questions on incentivizing sample sharing, improving consent processes, and collaborating to increase sample donations.
Similar to A personal perspective on open access publishing (20)
Innovations in Sequencing & Bioinformatics
Talk for
Healthy Central Valley Together Research Workshop
Jonathan A. Eisen University of California, Davis
January 31, 2024 linktr.ee/jonathaneisen
Talk by Jonathan Eisen for LAMG2022 meetingJonathan Eisen
The document discusses the history of the Lake Arrowhead Microbial Genomes (LAMG) conference. It reveals that LAMG2020 was cancelled due to a secret plan by organizers who formed an "anti-karyote society" that hates eukaryotes. The meeting was to be renamed the "Big, Large, Enormous" meeting of the Lake Arrowhead Big Large Enormous Anti-Karyote Society. The document also hints that several past LAMG speakers have made cryptic comments indicating involvement in a conspiracy surrounding the conference.
Thoughts on UC Davis' COVID Current ActionsJonathan Eisen
Slides I used for a presentation to Chancellor May's leadership council about the current state of UC Davis' response to COVID and how it could be improved
Phylogenetic and Phylogenomic Approaches to the Study of Microbes and Microbi...Jonathan Eisen
The document discusses Jonathan Eisen's work as a microbiology professor at UC Davis. It provides an overview of his research topics, which include microbial phylogenomics and evolvability, phylogenetic methods and tools, and using phylogenomics to study microbial communities and interactions between microbes and hosts under stress. The document also acknowledges collaborators and funding sources for Eisen's research over the years.
This document summarizes a class on detecting, quantifying, and tracking variations of SARS-CoV-2 RNA from COVID-19 samples. It discusses using quantitative RT-PCR (qRT-PCR) to detect and measure viral RNA levels in samples. Sequencing is used to identify variations in the viral genome over time, and online tools like Nextstrain allow viewing the evolution and global transmission of variants. Genotyping assays are also described that can rapidly screen samples for known single nucleotide variations during PCR.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Winter2020 Class 8 - COVID RNA DetectionJonathan Eisen
This document summarizes a class on SARS-CoV-2 RNA detection, quantification, and variation. It discusses how qRT-PCR is used to detect and quantify the virus by amplifying and detecting viral RNA. It also covers sequencing to identify variants, how variants evolve over time, and genotyping assays that can screen samples for known single nucleotide variations. Nextstrain and other online tools are presented that use sequencing data to analyze viral phylogenies, track variant distributions globally, and visualize genetic variations across the SARS-CoV-2 genome.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms for those who already suffer from conditions like depression and anxiety.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Winter2020 Class 5 - COVID VaccinesJonathan Eisen
The document discusses a class on COVID-19 vaccines. It covers topics like vaccine development, current candidates, delivery challenges, and comparisons between vaccines. Moderna and Pfizer mRNA vaccines are highlighted as being similar but having some differences in mRNA region, nanoparticle structure/synthesis, dosage amount, and storage temperature requirements. Other vaccines discussed include Novavax using spike protein nanoparticles, and AstraZeneca and Johnson & Johnson using DNA for spike protein delivered by a modified virus.
EVE198 Winter2020 Class 9 - COVID TransmissionJonathan Eisen
This document discusses modes of SARS-CoV-2 transmission including droplets, aerosols, and surfaces. It emphasizes that surfaces are not as big a risk as initially thought. It provides guidance on limiting transmission from different modes such as distancing, masks, washing hands, cleaning surfaces, and improving ventilation. The focus in 2021 is on droplets and aerosols rather than surfaces.
EVE198 Fall2020 "Covid Mass Testing" Class 8 VaccinesJonathan Eisen
This document discusses a class on vaccines for COVID-19. It covers topics like vaccine development, current candidate vaccines, challenges with vaccine distribution, and how vaccines are being assessed for safety, effectiveness, costs and production feasibility. Over 100 vaccine candidates are in development using platforms like DNA, RNA, viral vectors and inactivated viruses. Efforts like Operation Warp Speed are coordinating development of nucleic acid, viral vector and protein subunit vaccines. Distribution challenges include vaccine production, storage and logistics, number of doses required, and overcoming vaccine nationalism and hesitancy.
EVE198 Fall2020 "Covid Mass Testing" Class 2: Viruses, COIVD and TestingJonathan Eisen
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Fall2020 "Covid Mass Testing" Class 1 IntroductionJonathan Eisen
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
it describes the bony anatomy including the femoral head , acetabulum, labrum . also discusses the capsule , ligaments . muscle that act on the hip joint and the range of motion are outlined. factors affecting hip joint stability and weight transmission through the joint are summarized.
How to Fix the Import Error in the Odoo 17Celine George
An import error occurs when a program fails to import a module or library, disrupting its execution. In languages like Python, this issue arises when the specified module cannot be found or accessed, hindering the program's functionality. Resolving import errors is crucial for maintaining smooth software operation and uninterrupted development processes.
Executive Directors Chat Leveraging AI for Diversity, Equity, and InclusionTechSoup
Let’s explore the intersection of technology and equity in the final session of our DEI series. Discover how AI tools, like ChatGPT, can be used to support and enhance your nonprofit's DEI initiatives. Participants will gain insights into practical AI applications and get tips for leveraging technology to advance their DEI goals.
Strategies for Effective Upskilling is a presentation by Chinwendu Peace in a Your Skill Boost Masterclass organisation by the Excellence Foundation for South Sudan on 08th and 09th June 2024 from 1 PM to 3 PM on each day.
How to Build a Module in Odoo 17 Using the Scaffold MethodCeline George
Odoo provides an option for creating a module by using a single line command. By using this command the user can make a whole structure of a module. It is very easy for a beginner to make a module. There is no need to make each file manually. This slide will show how to create a module using the scaffold method.
A review of the growth of the Israel Genealogy Research Association Database Collection for the last 12 months. Our collection is now passed the 3 million mark and still growing. See which archives have contributed the most. See the different types of records we have, and which years have had records added. You can also see what we have for the future.
বাংলাদেশের অর্থনৈতিক সমীক্ষা ২০২৪ [Bangladesh Economic Review 2024 Bangla.pdf] কম্পিউটার , ট্যাব ও স্মার্ট ফোন ভার্সন সহ সম্পূর্ণ বাংলা ই-বুক বা pdf বই " সুচিপত্র ...বুকমার্ক মেনু 🔖 ও হাইপার লিংক মেনু 📝👆 যুক্ত ..
আমাদের সবার জন্য খুব খুব গুরুত্বপূর্ণ একটি বই ..বিসিএস, ব্যাংক, ইউনিভার্সিটি ভর্তি ও যে কোন প্রতিযোগিতা মূলক পরীক্ষার জন্য এর খুব ইম্পরট্যান্ট একটি বিষয় ...তাছাড়া বাংলাদেশের সাম্প্রতিক যে কোন ডাটা বা তথ্য এই বইতে পাবেন ...
তাই একজন নাগরিক হিসাবে এই তথ্য গুলো আপনার জানা প্রয়োজন ...।
বিসিএস ও ব্যাংক এর লিখিত পরীক্ষা ...+এছাড়া মাধ্যমিক ও উচ্চমাধ্যমিকের স্টুডেন্টদের জন্য অনেক কাজে আসবে ...
The simplified electron and muon model, Oscillating Spacetime: The Foundation...RitikBhardwaj56
Discover the Simplified Electron and Muon Model: A New Wave-Based Approach to Understanding Particles delves into a groundbreaking theory that presents electrons and muons as rotating soliton waves within oscillating spacetime. Geared towards students, researchers, and science buffs, this book breaks down complex ideas into simple explanations. It covers topics such as electron waves, temporal dynamics, and the implications of this model on particle physics. With clear illustrations and easy-to-follow explanations, readers will gain a new outlook on the universe's fundamental nature.
This slide is special for master students (MIBS & MIFB) in UUM. Also useful for readers who are interested in the topic of contemporary Islamic banking.
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Date: May 29, 2024
Tags: Information Security, ISO/IEC 27001, ISO/IEC 42001, Artificial Intelligence, GDPR
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5. Public Library of Science (PLoS)
• Started in 2000 by
– Harold Varmus
– Pat Brown
– Michael Eisen
• First action was to circulate an
open letter on publishing
6. The Letter
We support the establishment of an online public library that would
provide the full contents of the published record of research and
scholarly discourse in medicine and the life sciences in a freely accessible,
fully searchable, interlinked form. Establishment of this public library would
vastly increase the accessibility and utility of the scientific literature,
enhance scientific productivity, and catalyze integration of the disparate
communities of knowledge and ideas in biomedical sciences.We recognize
that the publishers of our scientific journals have a legitimate right to a fair
financial return for their role in scientific communication. We believe,
however, that the permanent, archival record of scientific research and
ideas should neither be owned nor controlled by publishers, but should
belong to the public and should be freely available through an international
online public library.To encourage the publishers of our journals to support
this endeavor, we pledge that, beginning in September 2001, we will
publish in, edit or review for, and personally subscribe to only those
scholarly and scientific journals that have agreed to grant
unrestricted free distribution rights to any and all original research
reports that they have published, through PubMed Central and similar
online public resources, within 6 months of their initial publication date.
7. The Letter
We support the establishment of an online public library that would
provide the full contents of the published record of research and
scholarly discourse in medicine and the life sciences in a freely accessible,
fully searchable, interlinked form. Establishment of this public library would
vastly increase the accessibility and utility of the scientific literature,
enhance scientific productivity, and catalyze integration of the disparate
communities of knowledge and ideas in biomedical sciences.We recognize
that the publishers of our scientific journals have a legitimate right to a fair
financial return for their role in scientific communication. We believe,
however, that the permanent, archival record of scientific research and
ideas should neither be owned nor controlled by publishers, but should
belong to the public and should be freely available through an international
online public library.To encourage the publishers of our journals to support
this endeavor, we pledge that, beginning in September 2001, we will
publish in, edit or review for, and personally subscribe to only those
scholarly and scientific journals that have agreed to grant
unrestricted free distribution rights to any and all original research
reports that they have published, through PubMed Central and similar
online public resources, within 6 months of their initial publication date.
8.
9.
10. PLoS After the Letter (2003)
• > 25,000 people signed the letter
• Small increase in open access support
• But not enough
• So PLoS announced the launch of their
own journals
– PLoS Biology
– PLoS Medicine
11. Me and PLoS
• Joined founding
Editorial Board of
PLoS Biology
• Still not fully
convinced about need
for OA
• Worried more about
User agrees to
not publish push for full “Open
genome level Science”
analyses
12. Ft. Lauderdale Agreement
• Feb 2003 meeting in Ft. Lauderdale on “Genome
Sequencing Data Release Policies”
• Follow up to the “Bermuda Accord”
• Debate about how open to be with data
• NHGRI had supported a similar policy to TIGRs (see
http://www.genome.gov/10506537)
• Sean Eddy gave a talk that convinced me that these
restrictions we in direct conflict with the whole point of
giving money to places to generate the data
• So I did what any scientist should do - some experiments
13. Open Data Experiment
• Unrestricted data access
policy on Tetrahymena
thermophila
• First time done at TIGR
• Many people published
papers before we did
• But many more helped
with our paper
Thanks for the message about
1 The Institute for Genomic Research, Rockville, Maryland, United States of America, 2
Department of Biology, York University, Toronto, Ontario, Canada, 3 Centre for Research in Mass
the genome, that is a nice
Spectrometry, York University, Toronto, Ontario, Canada, 4 Department of Biological Sciences,
Marquette University, Milwaukee, Wisconsin, United States of America, 5 Razavi-Newman Center
for Bioinformatics, The Salk Institute for Biological Studies, San Diego, California, United States of
America, 6 Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago,
surprise. Lots of Bacillus DNA in
Illinois, United States of America, 7 Department of Biology, Harvey Mudd College, Claremont,
California, United States of America, 8 Department of Biology, University of Texas at San Antonio,
San Antonio, Texas, United States of America, 9 Department of Electrical Engineering, University
there unfortunately but we are
of Texas at San Antonio, San Antonio, Texas, United States of America, 10 Department of
Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States
of America, 11 Department of Computer Science and Engineering, University of Washington,
Seattle, Washington, United States of America, 12 Department of Cellular Biology, University of
going to go wild looking in it.
Georgia, Athens, Georgia, United States of America, 13 Department of Biological Sciences,
University of Iowa, Iowa City, Iowa, United States of America, 14 Department of Biology,
University of Rochester, Rochester, New York, United States of America, 15 Canadian Institute for
Advanced Research, Department of Botany, University of British Columbia, Vancouver, British
Columbia, Canada, 16 Department of Genetics, Stanford University, Stanford, California, United
States of America, 17 Department of Molecular, Cellular, and Developmental Biology, University of
Patrick
California Santa Barbara, Santa Barbara, California, United States of America
14. Open Access Experiment
• Had published one paper in an Open
Access journal (Genome Biology)
• We were working on a paper on the
WMD - the first Wolbachia genome
Wolbachia of • Wolbachia are maternally transmitted
Male Destruction parasites that target males in many
species
• In filarial nematodes appear to be
mutualistic symbionts
• Our paper was being recruited by
Nature and Science
17. Experiments in Progress …
• But still unclear to me whether this Open
Access thing was a good idea or not
• Then real life intervened
18.
19. RhoGam
• Supplier
– RhoGAM should be administered within 72 hours of
known or suspected exposure to Rh-positive red blood
cells.
• Wikipedia
– It is given by intramuscular injection as part of modern
routine antenatal care at about 28 weeks of pregnancy,
and within 72 hours after childbirth.[5] It is also given
after antenatal pathological events that are likely to
cause a feto-maternal hemorrhage.[6]
• Question
– What happens if you do it even later?
20.
21.
22. You can purchase online access to
this article (and all its versions) for a
24-hour period. Articles are US $
29.95, with some exceptions where
prices may vary. Click "Buy Now" to
display the price
23.
24.
25. Access Blocked - What Next?
• Bought lots of articles
• Tried to contact experts
• Got friends to get some articles from libraries
• Got more and more pissed off
26. Medical Guesswork
• Wife got Rhogam 11 days after blood exposure
• Other treatments became in part guesswork as
well
• Note, doctors at this time were spectacular
• They even asked for assistance in finding out
answers to some treatment questions
• In theory, the scientific / medical literature could
help ....
28. Lack of Access
• Scientist without access
• Would access have helped?
• Is limiting access useful or needed?
• Goal of much of scientific and medical
research is to spread knowledge
31. Many Flavors of
Accessibility and Openness
• Free in University repositories
• Free on journal web site after six months
(e.g., Genome Research)
• Free on journal web site with registration
(e.g., Science)
• Free in PubMed Central after 6 months (e.g.,
ASM journals)
• Free and unrestricted everywhere
immediately (e.g., PLoS and BMC)
32. Many Flavors of
Accessibility and Openness
Cost Free $, $$, or $$$
Timing of free Immediate Later
Location Archives Journal site
Reuse Unrestricted Restricted
Copyright Author Journal
Who archives Journal Individual
33. Green Access
Cost Free $, $$, or $$$
Timing of free Immediate Later
Location Archives Journal site
Reuse Unrestricted Restricted
Copyright Author Journal
Who archives Journal Individual
34. Gold /Open Access
Cost Free $, $$, or $$$
Timing of free Immediate Later
Location Archives Journal site
Reuse Unrestricted Restricted
Copyright Author Journal
Who archives Journal Individual
Based on the Bethesda Principles, April 2003
35. Open Access
• Free, immediate access online
Unrestricted distribution and re-use
Author retains rights to attribution
Papers are immediately deposited in a
public online archive, such as PubMed Central
Bethesda Principles, April 2003
36. Biomed Central
• Commercial open access publisher
• Launched first open access journals in 2000
• Now publish >160 OA titles
• Purchased by Springer-Verlag in October 2008
• CEO: “This acquisition reinforces the fact that we
see open access publishing as a sustainable part of
STM publishing, and not an ideological crusade. “
37.
38. PLoS Biology
October, 2003
PLoS Medicine
October, 2004
PLoS Community Journals
June-September, 2005 October, 2007
40. Gold Open Access
Cost Free $, $$, or $$$
Timing of free Immediate Later
Location Archives Journal site
Reuse Unrestricted Restricted
Copyright Author Journal
Who archives Journal Individual
Based on the Bethesda Principles, April 2003
42. “Ten million American
adults look online for
health information on a
From the Pew Research Center
Seeking Health On-line 2006 study
http://pewresearch.org/reports/?ReportID=65
43. Everyone should have access to
research findings
• “It is not for either publishers or academics to
decide who should, and who should not, be
allowed to read scientific journal articles. We are
encouraged by the growing interest in research
findings shown by the public. It is in society’s
interest that public understanding of science
should increase. Increased public access to
research findings should be encouraged by
publishers, academics and Government alike”
• HoC S&T Committee Report, July 2004
44. The inspiration for Free Access is
not a new idea
“I want a poor student to have the same means
of indulging his learned curiosity,
of following his rational pursuits,
of consulting the same authorities,
of fathoming the most intricate inquiry
as the richest man in the kingdom…”
Antonio Panizzi, 1836
Principle Librarian of the British Museum
46. Timing of Access
• NIH and other guidelines now require
access after six months
• Delay supposedly improves ability of
journals to maintain subscriptions
• Immediate OA is the way science should
work
– Public and others can get engaged when press
coverage occurs
– Science happens rapidly
– Articles there whenever you look
49. Self-archiving sluggishness
• “Of the authors who have not yet self-
archived any articles, 71% remain unaware
of the option.”
– Alma Swan and Sheridan Brown, Open access self-
archiving: An author study
– http://cogprints.org/4385/
Slide based on one by Peter Suber
55. Copyright Issues
1. Authors are the copyright holders until they transfer
away their rights.
2. Transferring full copyright to a publisher gives the OA
decision to the publisher.
3. Many journals will alter the standard contract when
asked.
Slide based on one by Peter Suber
64. You can purchase online access to
this article (and all its versions) for a
24-hour period. Articles are US $
29.95, with some exceptions where
prices may vary. Click "Buy Now" to
display the price
65.
66.
67.
68.
69. You can purchase online access to
this article (and all its versions) for a
24-hour period. Articles are US $
29.95, with some exceptions where
prices may vary. Click "Buy Now" to
display the price
74. Text mining and open access
“So far, more that 90% of all biomedical literature
mining has been based on Medline, mainly because it is
freely available in a convenient format.”
“…future methods should be able to extract
information from the full text of papers…”
“However, it is restricted access to the full text of
papers…that is currently the greatest limitation…”
Jensen, Saric and Bork Nature Reviews Genetics
Feb 2006
76. Educational Benefits of OA
• No debate about “fair use”
• No need for password’s or logins for course
web sites
• No lawyers have to be involved
• Material from OA publications can be
repackaged for any purpose
78. Issues in Publishing
• Canceling subscriptions?
• End of surrogate metrics?
– Journal impact factor vs. article impact factor
– Need to change tenure, promotion, etc systems
to assess quality of work
• Funding for publishing
– OA is sustainable
– But still not free
• Peer review
– Pre vs. post-publication?
79. Open Access and Open Science
• Related but not the same things
• Open science examples
– OA publishing
– Open source software
– Open data release
– Open notebooks
– Open materials and methods
• All can be good things, but even if against
one you can support the others
80. What can you do so support OA?
• Publishing
– Try it and/or shift to more and more OA
– Quit non OA cold turkey
• Service
– Do not review for non OA journals
– If involved in journal, work to change OA policies
• Lobby
– Push for OA at your Institution and with government
• Hiring
– Give credit for OA publishing
– Same as you would do for data, software release
• Education
– Use CC material freely
Editor's Notes
One of leaders of open access movement.
Giving everyone access to information is not a new idea - the quote is from an influential librarian in the 19th century.
May 2005
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
One more: publishers don’t need full copyright
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
A word about copyright – this is the license we use.
It’s very important that authors do pay attention to this issue – the signing of a more restrictive license limits the uses to which the literature can be put.
So how does it work? Publishing costs money, so how are we going to fund it.
Subscription based publishing works like this – there is a financial barrier to reading literature, and that money is paid by funding agencies, institutions, and ultimately by the government.
With OA, that payment step is moved up the chain – the sources of funding stay the same, the cost stays the same (or probably comes down). But by having the payment made earlier, no money needs to be paid to access the literature.
Central to this idea – publishing is an integral part of the research process
So the challenge is to alter the way publishing is funded – not how much money is needed.