How to find data for your research
Presented by Fiona Nielsen at the International Conference of Genomics 2016 www.icg-11.org in the session Data Sharing and Analysis chaired by Laurie Goodman, editor-in-chief, GigaScience
From bioinformatics scientist to entrepreneur - Women in Omics - ICG11 - 2016Fiona Nielsen
Presented by Fiona Nielsen at the International Conference of Genomics at China National Genebank, Shenzhen http://www.icg-11.org
I present the "WHY" of what I am doing, and how I got here. A personal story of frustration, science and family.
Session chaired by Laurie Goodman, Gigascience
From Bioinformatics Scientist to EntrepreneurFiona Nielsen
A 15min presentation at the University of Southern Denmark (SDU) Alumni career event on May 28th, 2016.
Thanks to Jørgen Bang Nielsen and IMADA for organising.
Read more:
- SDU http://www.sdu.dk
- Institute for mathematics and computer science (IMADA): http://imada.sdu.dk
- DNAdigest http://DNAdigest.org
- Repositive http://repositive.io
SciDataCon - How to increase accessibility and reuse for clinical and persona...Fiona Nielsen
Presented in session 48 - Sharing of sensitive data - presented by Fiona Nielsen on September 12, 2016 at #SciDataCon http://scidatacon.org
We have addressed the most pressing problem for public genomic data, that of data discoverability, by indexing worldwide resources for genomic research data on an online platform (repositive.io) providing a single point of entry to find and access available genomic research data.
http://www.scidatacon.org/2016/sessions/48/paper/26/
http://www.scidatacon.org/2016/sessions/48/
International data week - #RDAPlenary #IDW2016
Overcoming barriers for genomic data sharing yaac presentation may 23 2015Fiona Nielsen
Overcoming barriers for genomic data sharing - presented at Young Alliance Against Cancer conference on May 23rd 2015 in Copenhagen. http://young-alliance.org
Repositive is a mission-driven company aiming to facilitate data sharing for genomics research via the online platform http://repositive.io
Repositive was spun out of the charity DNAdigest.
Read more: http://dnadigest.org/repositive-raises-300k-for-genomics-platform/
Find us on Twitter @repositiveio and @DNAdigest
This is a presentation that I delivered at the ACS Division of Chemical Information meeting regarding "Reproducibility, Reporting, Sharing & Plagiarism".
I took the opportunity to remove my hat that has me be the VP of Strategic Development at RSC, and a member of the cheminformatics group that built ChemSpider and works on other RSC projects related to it. Instead I presented on how a LACK OF MANDATES from publishers on me in terms of submission of data accompanying articles I am involved with writing is actually weakening my scientific record as data is not getting shared in the most useful forms possible to the benefit of the community. I think there would be benefits for publishers to start pushing me for MORE data, in fairly general standards, and allowing me (and others) to download the data in the form of molecules (and collections), spectral data, CSV files etc.
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. We have delivered public access to terabytes of open data, as well to a large number of publicly accessible databases and applications, to support the research efforts for a large community of scientists. Many of our contributions to science are summarily described in research papers but to date we have not optimized our contributions to inform altmetrics statistics associated with our work. Critically missing from altmetrics is access to our numerous software applications and web service accesses, as well as the growing importance of our experimental data and models (e.g ToxCast, ExpoCast, DSSTox and others) to the scientific and regulatory communities. This presentation will provide an overview of our efforts to more fully understand, and quantify, our impact on the environmental sciences using a combination of our measurement approaches and available altmetrics tools. This abstract does not reflect U.S. EPA policy.
With the flourishing environment of platforms for sharing data, establishing an online profile and engaging in scientific discourse through alternative modes of publishing and participation, there are numerous potential benefits. However, while many scientists invest significant amounts of time in sharing their activities and opinions with friends and family the majority do not make use of the new opportunities to participate in the developing social web of science, despite the potential impact and influence on future careers. We now have many new ways to contribute to science outside of the classical publishing model. These include the ability to annotate and curate data, to “publish” in new ways on blogs and micropublishing sites, and many of these activities can be as part of a growing crowdsourcing network. Our efforts in this area are already being indexed and exposed on the internet via our publications, presentations and data and increasingly we are being quantified. This presentation will provide an overview of the various types of networking and collaborative sites available to scientists and ways to expose their scientific activities online. Many of these can ultimately contribute to the developing metrics of a scientist as identified in the new world of alternative metrics. Participation offers a great opportunity to develop a scientific profile within the community and may ultimately be very beneficial, especially to scientists early in their career.
On Friday September 16th I was honored with the award for the North Carolina American Chemical Society Distinguished Speaker Award and got to review the past 20 years of my career. This was my short intro bio
"Antony Williams is a Ph.D. NMR spectroscopist and cheminformatician who has worked in academia, government, a Fortune 500 company, and two start-ups. He is co-founder of the free online chemical database ChemSpider, originally started as a hobby project and ultimately acquired by the Royal Society of Chemistry (in the UK) and now used by over 50,000 users per day. He is now a computational chemist at the Environmental Protection Agency in the National Center for Computational Toxicology and is focused on developing web applications to support data dissemination and progress efforts in allowing for faster and cheaper approaches to identify potential toxicological effects of chemicals. He has published >180 papers, >25 book chapters and a number of books. He is known as the ChemConnector on social networks. "
From bioinformatics scientist to entrepreneur - Women in Omics - ICG11 - 2016Fiona Nielsen
Presented by Fiona Nielsen at the International Conference of Genomics at China National Genebank, Shenzhen http://www.icg-11.org
I present the "WHY" of what I am doing, and how I got here. A personal story of frustration, science and family.
Session chaired by Laurie Goodman, Gigascience
From Bioinformatics Scientist to EntrepreneurFiona Nielsen
A 15min presentation at the University of Southern Denmark (SDU) Alumni career event on May 28th, 2016.
Thanks to Jørgen Bang Nielsen and IMADA for organising.
Read more:
- SDU http://www.sdu.dk
- Institute for mathematics and computer science (IMADA): http://imada.sdu.dk
- DNAdigest http://DNAdigest.org
- Repositive http://repositive.io
SciDataCon - How to increase accessibility and reuse for clinical and persona...Fiona Nielsen
Presented in session 48 - Sharing of sensitive data - presented by Fiona Nielsen on September 12, 2016 at #SciDataCon http://scidatacon.org
We have addressed the most pressing problem for public genomic data, that of data discoverability, by indexing worldwide resources for genomic research data on an online platform (repositive.io) providing a single point of entry to find and access available genomic research data.
http://www.scidatacon.org/2016/sessions/48/paper/26/
http://www.scidatacon.org/2016/sessions/48/
International data week - #RDAPlenary #IDW2016
Overcoming barriers for genomic data sharing yaac presentation may 23 2015Fiona Nielsen
Overcoming barriers for genomic data sharing - presented at Young Alliance Against Cancer conference on May 23rd 2015 in Copenhagen. http://young-alliance.org
Repositive is a mission-driven company aiming to facilitate data sharing for genomics research via the online platform http://repositive.io
Repositive was spun out of the charity DNAdigest.
Read more: http://dnadigest.org/repositive-raises-300k-for-genomics-platform/
Find us on Twitter @repositiveio and @DNAdigest
This is a presentation that I delivered at the ACS Division of Chemical Information meeting regarding "Reproducibility, Reporting, Sharing & Plagiarism".
I took the opportunity to remove my hat that has me be the VP of Strategic Development at RSC, and a member of the cheminformatics group that built ChemSpider and works on other RSC projects related to it. Instead I presented on how a LACK OF MANDATES from publishers on me in terms of submission of data accompanying articles I am involved with writing is actually weakening my scientific record as data is not getting shared in the most useful forms possible to the benefit of the community. I think there would be benefits for publishers to start pushing me for MORE data, in fairly general standards, and allowing me (and others) to download the data in the form of molecules (and collections), spectral data, CSV files etc.
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. We have delivered public access to terabytes of open data, as well to a large number of publicly accessible databases and applications, to support the research efforts for a large community of scientists. Many of our contributions to science are summarily described in research papers but to date we have not optimized our contributions to inform altmetrics statistics associated with our work. Critically missing from altmetrics is access to our numerous software applications and web service accesses, as well as the growing importance of our experimental data and models (e.g ToxCast, ExpoCast, DSSTox and others) to the scientific and regulatory communities. This presentation will provide an overview of our efforts to more fully understand, and quantify, our impact on the environmental sciences using a combination of our measurement approaches and available altmetrics tools. This abstract does not reflect U.S. EPA policy.
With the flourishing environment of platforms for sharing data, establishing an online profile and engaging in scientific discourse through alternative modes of publishing and participation, there are numerous potential benefits. However, while many scientists invest significant amounts of time in sharing their activities and opinions with friends and family the majority do not make use of the new opportunities to participate in the developing social web of science, despite the potential impact and influence on future careers. We now have many new ways to contribute to science outside of the classical publishing model. These include the ability to annotate and curate data, to “publish” in new ways on blogs and micropublishing sites, and many of these activities can be as part of a growing crowdsourcing network. Our efforts in this area are already being indexed and exposed on the internet via our publications, presentations and data and increasingly we are being quantified. This presentation will provide an overview of the various types of networking and collaborative sites available to scientists and ways to expose their scientific activities online. Many of these can ultimately contribute to the developing metrics of a scientist as identified in the new world of alternative metrics. Participation offers a great opportunity to develop a scientific profile within the community and may ultimately be very beneficial, especially to scientists early in their career.
On Friday September 16th I was honored with the award for the North Carolina American Chemical Society Distinguished Speaker Award and got to review the past 20 years of my career. This was my short intro bio
"Antony Williams is a Ph.D. NMR spectroscopist and cheminformatician who has worked in academia, government, a Fortune 500 company, and two start-ups. He is co-founder of the free online chemical database ChemSpider, originally started as a hobby project and ultimately acquired by the Royal Society of Chemistry (in the UK) and now used by over 50,000 users per day. He is now a computational chemist at the Environmental Protection Agency in the National Center for Computational Toxicology and is focused on developing web applications to support data dissemination and progress efforts in allowing for faster and cheaper approaches to identify potential toxicological effects of chemicals. He has published >180 papers, >25 book chapters and a number of books. He is known as the ChemConnector on social networks. "
Data for Science: How Elsevier is using data science to empower researchersPaul Groth
Each month 12 million people use Elsevier’s ScienceDirect platform. The Mendeley social network has 4.6 million registered users. 3500 institutions make use of ClinicalKey to bring the latest in medical research to doctors and nurses. How can we help these users be more effective? In this talk, I give an overview of how Elsevier is employing data science to improve its services from recommendation systems, to natural language processing and analytics. While data science is changing how Elsevier serves researchers, it’s also changing research practice itself. In that context, I discuss the impact that large amounts of open research data are having and the challenges researchers face in making use of it, in particular, in terms of data integration and reuse. We are at just beginning to see of how technology and data is changing science correspondingly this impacts how best to empower those who practice it.
Presented by Joan Kolarik (Weizmann Institute, Israel) at the seminar "When Open Science Meets Big Data: Adjustment of Library Services" (Teldan Info: The 33rd Annual Conference & Exhibition on May, 16th 2018, Israel).
This is a joint presentation by Jeroen Bosman and Bianca Kramer, given during a joint NISO-ICSTI webinar, held on Wednesday, October 26, on Enabling Innovation in Researcher Workflow and Scholarly Communication.
Genome sharing projects around the world nijmegen oct 29 - 2015Fiona Nielsen
Genome sharing projects across the world
Did you ever wonder what happened to the exponential increase in genome sequencing data? It is out there around the world and a lot of it is consented for research use. This means that if you just know where to find the data, you can potentially analyse gigabytes of data to power your research.
In this talk Fiona will present community genome initiatives, the genome sharing projects across the world, how you can benefit from this wealth of data in your work, and how you can boost your academic career by sharing and collaboration.
by Fiona Nielsen, Founder and CEO of DNAdigest and Repositive
With a background in software development Fiona pursued her career in bioinformatics research at Radboud University Nijmegen. Now a scientist-turned-entrepreneur Fiona founded DNAdigest and its social enterprise spin-out Repositive Ltd. Both the charity and company focus on efficient and ethical sharing of genetics data for research to accelerate diagnostics and cures for genetic diseases.
Given at the NIH stock center directors meeting, August 8, 2016. Author: Anita Bandrowski
Project: Resource Identification Initiative http://scicrunch.org/resources
Topic: How is model organism data being used in literature
Access to Freely Available Journal Articles: Gold, Green, and Rogue Open Ac...Jason Price, PhD
A recent bibliometrics study found that 54% of 4.6 million scientific papers from peer-reviewed journals indexed in Scopus during the years 2011-2013 could be downloaded for free on the internet in April of 2014 (Archambault, et al. 2014). As time rolls on, authors and researchers are increasingly using more-and-less legal scholarly article sharing services to "take back the literature," or even just to access it more conveniently (Bohannon, 2016). The objective of this study was to evaluate a manageable sample of journal articles across the sciences, social sciences and humanities for their availability in gold, green and rogue open access forms, including ResearchGate and Sci-Hub. Attendees will gain a greater appreciation of the extent of open access availability through Google Scholar, Google and commercial discovery systems, and will be challenged to roll with the times by expanding the role of libraries in broadening access to the freely available literature.
This presentation was provided by Emma Ganley of the Public Library of Science during the August 10 NISO-NASIG webinar, How Librarians Use, Support and Can Implement Researcher Identifiers.
At this time, and in a culture where online access is now an imperative, Wikipedia has become the definitive encyclopedia. In terms of its support for chemistry it is rich in many encyclopedic pages including named reactions, chemical and drug pages, articles about chemists, and many other forms of chemistry related information. Wikipedia is hosted on Mediawiki, an open source platform that can be utilized by anybody as the basis of their own hosted content collection. Mediawiki has been used as a collaborative environment by a number of chemists to create As a general contribution to the community Mediawiki has been used to create a number of resources that have become very popular with the chemistry community. These include VIPEr to support inorganic chemistry, ChemWiki as an online textbook and other educational resources and a Chemical Information Wikibook. Mediawiki has also been used by the author to host open source collections of data including scientists, scientific databases and mobile apps for science: the ScientistsDB, SciDBs and SciMobileApps wikis. This presentation will provide an overview of some of the chemistry resources that presently exist and celebrate the major contributions that Wikipedia and Mediawiki have made to the collaborative dissemination of chemistry.
A presentation about Digital Repository @ Iowa State University to faculty from Iowa State University's College of Veterinary Medicine, February 20, 2013.
Librarians supporting applied research and discipline-specific researchersLibrary_Connect
On March 13, 2014, three chemistry PhDs presented a Library Connect webinar on “Librarians supporting applied research and discipline-specific researchers.” The presenters included:
Oliver Renn, Head of the Chemistry | Biology | Pharmacy Information Center, Dept. of Chemistry and Applied Biosciences, ETH Zürich
Jan Reedijk, Emeritus Professor of Chemistry, Leiden University and Professor of Chemistry at King Saud University in Riyadh
Ye Li, Chemistry Librarian, Shapiro Science Library, University of Michigan
More: http://ow.ly/uFI8H
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
Genome sharing projects around the world - Open Access is not enough Fiona Nielsen
Presented by Fiona Nielsen at the 2016 conference on Electronic Publishing #Elpub2016 in Goettingen, Germany, June 8th 2016
Take home message 1: Open Access does not equal discoverability
Take home message 2: Lots of genomic research data is not found and reused because it is not discoverable
Take home message 3: Repositive is a portal for searching for genomics data
Read more:
- EPUB conference http://meetings.copernicus.org/elpub2016/programme.html
- Repositive http://repositive.io
Data for Science: How Elsevier is using data science to empower researchersPaul Groth
Each month 12 million people use Elsevier’s ScienceDirect platform. The Mendeley social network has 4.6 million registered users. 3500 institutions make use of ClinicalKey to bring the latest in medical research to doctors and nurses. How can we help these users be more effective? In this talk, I give an overview of how Elsevier is employing data science to improve its services from recommendation systems, to natural language processing and analytics. While data science is changing how Elsevier serves researchers, it’s also changing research practice itself. In that context, I discuss the impact that large amounts of open research data are having and the challenges researchers face in making use of it, in particular, in terms of data integration and reuse. We are at just beginning to see of how technology and data is changing science correspondingly this impacts how best to empower those who practice it.
Presented by Joan Kolarik (Weizmann Institute, Israel) at the seminar "When Open Science Meets Big Data: Adjustment of Library Services" (Teldan Info: The 33rd Annual Conference & Exhibition on May, 16th 2018, Israel).
This is a joint presentation by Jeroen Bosman and Bianca Kramer, given during a joint NISO-ICSTI webinar, held on Wednesday, October 26, on Enabling Innovation in Researcher Workflow and Scholarly Communication.
Genome sharing projects around the world nijmegen oct 29 - 2015Fiona Nielsen
Genome sharing projects across the world
Did you ever wonder what happened to the exponential increase in genome sequencing data? It is out there around the world and a lot of it is consented for research use. This means that if you just know where to find the data, you can potentially analyse gigabytes of data to power your research.
In this talk Fiona will present community genome initiatives, the genome sharing projects across the world, how you can benefit from this wealth of data in your work, and how you can boost your academic career by sharing and collaboration.
by Fiona Nielsen, Founder and CEO of DNAdigest and Repositive
With a background in software development Fiona pursued her career in bioinformatics research at Radboud University Nijmegen. Now a scientist-turned-entrepreneur Fiona founded DNAdigest and its social enterprise spin-out Repositive Ltd. Both the charity and company focus on efficient and ethical sharing of genetics data for research to accelerate diagnostics and cures for genetic diseases.
Given at the NIH stock center directors meeting, August 8, 2016. Author: Anita Bandrowski
Project: Resource Identification Initiative http://scicrunch.org/resources
Topic: How is model organism data being used in literature
Access to Freely Available Journal Articles: Gold, Green, and Rogue Open Ac...Jason Price, PhD
A recent bibliometrics study found that 54% of 4.6 million scientific papers from peer-reviewed journals indexed in Scopus during the years 2011-2013 could be downloaded for free on the internet in April of 2014 (Archambault, et al. 2014). As time rolls on, authors and researchers are increasingly using more-and-less legal scholarly article sharing services to "take back the literature," or even just to access it more conveniently (Bohannon, 2016). The objective of this study was to evaluate a manageable sample of journal articles across the sciences, social sciences and humanities for their availability in gold, green and rogue open access forms, including ResearchGate and Sci-Hub. Attendees will gain a greater appreciation of the extent of open access availability through Google Scholar, Google and commercial discovery systems, and will be challenged to roll with the times by expanding the role of libraries in broadening access to the freely available literature.
This presentation was provided by Emma Ganley of the Public Library of Science during the August 10 NISO-NASIG webinar, How Librarians Use, Support and Can Implement Researcher Identifiers.
At this time, and in a culture where online access is now an imperative, Wikipedia has become the definitive encyclopedia. In terms of its support for chemistry it is rich in many encyclopedic pages including named reactions, chemical and drug pages, articles about chemists, and many other forms of chemistry related information. Wikipedia is hosted on Mediawiki, an open source platform that can be utilized by anybody as the basis of their own hosted content collection. Mediawiki has been used as a collaborative environment by a number of chemists to create As a general contribution to the community Mediawiki has been used to create a number of resources that have become very popular with the chemistry community. These include VIPEr to support inorganic chemistry, ChemWiki as an online textbook and other educational resources and a Chemical Information Wikibook. Mediawiki has also been used by the author to host open source collections of data including scientists, scientific databases and mobile apps for science: the ScientistsDB, SciDBs and SciMobileApps wikis. This presentation will provide an overview of some of the chemistry resources that presently exist and celebrate the major contributions that Wikipedia and Mediawiki have made to the collaborative dissemination of chemistry.
A presentation about Digital Repository @ Iowa State University to faculty from Iowa State University's College of Veterinary Medicine, February 20, 2013.
Librarians supporting applied research and discipline-specific researchersLibrary_Connect
On March 13, 2014, three chemistry PhDs presented a Library Connect webinar on “Librarians supporting applied research and discipline-specific researchers.” The presenters included:
Oliver Renn, Head of the Chemistry | Biology | Pharmacy Information Center, Dept. of Chemistry and Applied Biosciences, ETH Zürich
Jan Reedijk, Emeritus Professor of Chemistry, Leiden University and Professor of Chemistry at King Saud University in Riyadh
Ye Li, Chemistry Librarian, Shapiro Science Library, University of Michigan
More: http://ow.ly/uFI8H
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
Genome sharing projects around the world - Open Access is not enough Fiona Nielsen
Presented by Fiona Nielsen at the 2016 conference on Electronic Publishing #Elpub2016 in Goettingen, Germany, June 8th 2016
Take home message 1: Open Access does not equal discoverability
Take home message 2: Lots of genomic research data is not found and reused because it is not discoverable
Take home message 3: Repositive is a portal for searching for genomics data
Read more:
- EPUB conference http://meetings.copernicus.org/elpub2016/programme.html
- Repositive http://repositive.io
Workshop - finding and accessing data - Cambridge August 22 2016Fiona Nielsen
Finding and accessing human genomic data for research
University of Cambridge, United Kingdom | Seminar Room G
Monday, 22 August 2016 from 10:00 to 12:00 (BST)
Charlotte, Nadia and Fiona presented an overview of data sources around the world where you can find genomics data for your research and gave examples of the data access application for dbGaP and EGA with specific details relevant for University of Cambridge researchers.
Geke van Dijk, "Tugboats and Tankers: Contributing to Longterm Organizational...WebVisions
Contributing to longterm change in organisations and their service offering involves serious committment and stamina. You seldom see radical changes just on the basis of a single project. The results of that project might be mind blowing in itself, but in the longer term the effect of it on the wider organisation might seem disappointing.
Presented at WebVisions Barcelona 2013.
Offizielles Presse Kit der Pando Ventures GmbH. Bei Fragen wenden Sie sich bitte an Enrico Jakob (eja@pando.ventures). Pando investiert in junge Unternehmen im Rhein-Main Gebiet und unterstützt diese auf dem Weg in den Markt.
The following doodles walk you through a five step process that will challenge you to make more productive and effective decisions throughout the day.
Explore this topic in details at blog.IQmatrix.com/working-smarter
Finding and accessing human genome data with RepositiveManuel Corpas
The slides of the workshop I gave on May 29th 2017 at the European society for Human Genetics in Copenhagen, Denmark. Here I present the Repositive platform, a tool that helps scientist find and access human genome data.
Workshop finding and accessing data - fiona nadia charlotte - cambridge apr...Fiona 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.
Organised in collaboration between DNAdigest and Open Data Cambridge.
Read more about our work:
http://DNAdigest.org
http://repositive.io
https://uk.linkedin.com/in/fionanielsen
http://www.data.cam.ac.uk
Scott Edmunds slides from class 7 from the HKU Data Curation (module MLIM7350 from the Faculty of Education) course covering open data policy and practice, and the Hong Kong context.
Data dialogue - Human Genomic Data DiscoveryFiona Nielsen
Presenting at The Data Dialogue. Time to Share: Navigating Boundaries & Benefits - Afternoon session: Sharing difficult data.
July 28 - 2016 @ University of Cambridge
http://www.ses.ac.uk/event/data-dialogue-time-share-navigating-boundaries-benefits/
In this talk I present an overview of human genomic data sources around the world, their funding, access policies and type of data they contain. Discussing why data sharing is hard, including issues of data privacy and a research culture that does not incentivise sharing of data and results.
Presented by Fiona Nielsen, founder and CEO of Repositive
http://repositive.io
Scott Edmunds talk at AIST: Overcoming the Reproducibility Crisis: and why I ...GigaScience, BGI Hong Kong
Scott Edmunds talk at the AIST Computational Biology Research Center in Tokyo: Overcoming the Reproducibility Crisis: and why I stopped worrying a learned to love open data (& methods), July 1st 2014
What is research data?
Value and potential of research data and who benefits
What is data sharing? Open/shared/closed models
Benefits of open data
Class discussion: does all data need to be open to get value from it?
Scott Edmunds: Channeling the Deluge: Reproducibility & Data Dissemination in...GigaScience, BGI Hong Kong
Scott Edmunds talk at the 7th Internation Conference on Genomics: "Channeling the Deluge: Reproducibility & Data Dissemination in the “Big-Data” Era. ICG7, Hong Kong 1st December 2012
"
Recomendations for infrastructure and incentives for open science, presented to the Research Data Alliance 6th Plenary. Presenter: William Gunn, Director of Scholarly Communications for Mendeley.
Open Data in a Big Data World: easy to say, but hard to do?LEARN Project
Presentation at 3rd LEARN workshop on Research Data Management, “Make research data management policies work”
Helsinki, 28 June 2016, by Sarah Callaghan, STFC Rutherford Appleton Laboratory
Scott Edmunds slides for class 8 from the HKU Data Curation (module MLIM7350 from the Faculty of Education) course covering science data, medical data and ethics, and the FAIR data principles.
EICT Summer School August 2023 - Things I never knew I never knew - about bu...Fiona Nielsen
Expert workshop session delivered at IECT Summer School for Entrepreneurs on August 23, 2023, by Fiona Nielsen.
Fiona is a serial entrepreneur with lots of experience in hiring, leading and laying off people as part of her startup journey. In this presentation Fiona shares practical down to earth tips and examples on how to build a great team at your startup.
Topics include breakdowns of how to:
- Get great people on board
- Always improve your leadership
- Invest in good culture from the start
For example "1. Get great people on board"
Attract the right people to apply/express interest
Describe the role you are looking for and be specific about making the title reflect the job, e.g. “co-founder” or “marketing intern”
Always include the mission and vision of the company. Don’t fluff it.
Consider why anyone would work for you - beyond being paid a salary.
Great candidates have a choice of where to work, they will choose a place where they find meaning, feel motivated and challenged, and feel welcome.
Investing in innovation for genomic medicine - sept 5 2017Fiona Nielsen
Keynote at #TechBBQ 2017 by Fiona Nielsen
The journey of Repositive and how groundbreaking innovation is found in the crossover between traditional business and investment verticals.
Investing in innovation for genomic medicine - the journey of RepositiveFiona Nielsen
by Fiona Nielsen
Presented for UK Pharmacogenetics and Stratified Medicine Network (UK PGx Network) - Entrepreneurship, Disruptive Innovation and Personalised Medicine University of Liverpool London Campus, Finsbury Square, Wednesday 7th June 2017
Pistoia Alliance European Conference, Kings College London, April 19, 2016
Panel introduction to Big (Biomedical) Data and the challenges facing research in biomedical R&D with examples from genomics data around the world. #Pistoia2016
Event link:
https://www.eventbrite.co.uk/e/pistoia-alliance-european-conference-2016-tickets-19618953819
Read more about me and my work at:
http://dnadigest.org
http://repositive.io
https://uk.linkedin.com/in/fionanielsen
Why i left my job in genomics R&D - Lunteren - april 18 - 2016Fiona Nielsen
Career talk about how I moved from bioinformatics scientist to become an entrepreneur.
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
The need to redefine genomic data sharing - moving towards Open Science Oct ...Fiona Nielsen
This presentation was given at the symposium: Genomics for Health and Environment in Nijmegen on Oct 30, 2014
http://www.studiegids.science.ru.nl/2014/science/prospectus/biology_bachelor/course/34732/
The presentation introduces Open Science and Open Access Publishing and discusses these concepts in relation to (human) genomics.
The discussion includes a presentation of the concept behind http://repositive.io, the social enterprise software platform which was spun out of the DNAdigest research activities.
As a special edition to the students in the audience who are curious about their future scientific career, I included a couple of slides about my move from academic research to being a social entrepreneur.
DNAdigest works to promote and enable easier and more efficient sharing of genomics data for research. We educate and engage the community about the hurdles and dilemmas for data sharing as faced from the perspective of stakeholders in academia, industry and patient communities. As part of our work we are working with our community and supporters to prototype new mechanisms and concepts for data sharing and data access.
Please visit our website to learn more about our activities and events: http://DNAdigest.org
Follow us on twitter: @DNAdigest
DNAdigest Eagle Genomics Symposium March 27, 2014Fiona Nielsen
At the Eagle Genomics Symposium Fiona Nielsen CEO and founder of DNAdigest presented a discussion of the trade-off between privacy and open access and how hard-to-access data is hindering progress in genetics research.
Read more at http://DNAdigest.org and have a look at our campaign in support of collaborative open science for human genetics: http://tiny.cc/funddna <-- this is where you can get one of those cool #OpenScience T-shirts ;)
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
ICG-11 - genomic data projects around the world - nov 5 2016
1. ICG-11: Genomic Data Projects around the World
- How to find data for your research
Fiona Nielsen – November 4th 2016
2. We are always looking for data
Genetics,
Cancer,
Rare disease
research
We need
access to the
right data at
the right time
DNA
interpretation
requires
lots of data
3. How much data do you need to publish a paper?
2001: 1 human genome
2012: 1000 Genomes (1092 genomes, since increased to ~2500)
2015:
UK10K, Icelandic population (2,636 + 100k imputed),
Cancer genome atlas ~11,000 genomes
?
2016:
Exac consortium 65,000 exomes
GnomAD ~126,000 exomes
2020:
4. Data is not easy to find and access
FRAGMENTED
Poor visibility of available
genomic data
ADMIN BURDEN
Huge overhead to manage
data access
BAD CULTURE
Lack of data sharing habits in
research culture
5. Finding and accessing data can take months
40%
48%
11%
< 1 week
1-3 months
+6 months
Time spent data scouting per project
6. Why the barrier?
Barriers
• Difficult to find data, let alone
find the RIGHT data
• Time-consuming and difficult
to apply for access to data
• Complicated and labourious to
submit data to public
repositories
http://blog.repositive.io/tag/data-access/
http://blog.repositive.io/tag/data-sharing/
10. We have identified hundreds of data sources
Universities – Or repositories
affiliated to a university.
Projects/Consortia – Has a
specific purpose/aim. Often
focussed on a specific
research question or disease.
Public repositories – Allows
download and upload of
data from multiple
institutions.
Companies – For profit
organisations making data
available for free or as a
service.
Biobanks – many have sequence data of their biological samples.
Researchers
know on
average 4-5
data sources
More data sources appear every day,
to date we have identified 350+
11. Simpler workflow
for data access
And indexed them on a the Repositive platform
Discover and
access
Efficient Search,
see related results
Find colleagues &
their data interests
Co-annotate data &
community feedback
Free to use: http://discover.repositive.io
12. Platform launched in Sept 2016
Discover and
access
Efficient Search,
see related results
Find colleagues &
their data interests
Co-annotate data &
community feedback
1 Million+
Human genomic
datasets indexed
Free to use: http://discover.repositive.io
13. Platform launched in Sept 2016
Discover and
access
Efficient Search,
see related results
Find colleagues &
their data interests
Co-annotate data &
community feedback
1 Million+
datasets indexed
Simpler workflow
for data access
177k
Whole Exomes
213k
Whole Genomes
2400
23andMe samples
Free to use: http://discover.repositive.io
14. Platform launched in Sept 2016
Discover and
access
Efficient Search,
see related results
Find colleagues &
their data interests
Co-annotate data &
community feedback
1 Million+
datasets indexed
Simpler workflow
for data access
61+
Countries
426+
Research organisations
Using Repositive
PDX Consortium
With AstraZeneca
Free to use: http://discover.repositive.io
15. 11
155
2
2
4
4
7
780
0
5
10
15
20
25
30
35
40
45
GB FI NL FR DE CH EE BE DK ES SI IE SE
0
5
10
15
20
25
30
35
CA MD MA WA NY TX AZ DC NJ NC PA UT TN CO IN FL LA VA IL ME OH MO MI SC OR
1
1
1
1
1
1
Data sources across the globe
GEO location of 278
data sources analysed.
Found by tracking IP address
of the source.
These include:
Public Repositories
Universities
Companies
BioBanks
Research consortiums
18. Machines & Data sources
947
5600
88
660
26
68
50
62
3
25
0
0
23 International
Interesting site to look at:
http://omicsmaps.com/stats
19. • Repositive is supporting the whole research workflow
• Faster, more efficient data discovery
• Streamlining data access applications
• Developing technology for efficient data access
• Setting up pre-competitive data sharing agreements
• Running workshops and training programmes
More efficient data access
Read about our pre-competitive PDX data resource in collaboration with AstraZeneca http://repositive.io/pdx
20. Building upon best practices
MAKE DATA
DISCOVERABLE
SIMPLIFY
WORKFLOWS
CONTRIBUTE TO
COMMUNITY
DNAdigest and Repositive – Connecting the world of genomic data
http://www.tinyurl.com/plos-biology-repositive
First 30 data sources listed here:
21. Connecting the world of genomic data
Visit us at: http://repositive.io
Or tweet us @repositiveio Free to use: http://discover.repositive.io
Fiona Nielsen, CEO
Email us: info@repositive.io
Editor's Notes
Our mission is to speed up research and diagnostics for genetic diseases by enabling efficient and ethical access to genomic research data
Because interpretation requires LOTS of data
And although data exists around the world, it is siloed, and even if available, it is not accessible
This is Jenn, a genetic researcher –our target customer- seeking to interpret data from genetic diseases and cancer
She needs data from other patients to compare and interpret Mabels DNA
She also has data available in her own lab, but she cannot share because of concerns how to deal with secure access to sensitive data and vetting of users
Data is fragmented in unconnected silos – makes it very difficult to discover data
Tracking data and working with data access requests is a time-consuming and bureaucratic exercise
Difficult to build a user community without best practices and tools/platforms where users can share their data experience / findings
Because interpretation requires LOTS of data
And although data exists around the world, it is siloed, and even if available, it is not accessible
This is Jenn, a genetic researcher –our target customer- seeking to interpret data from genetic diseases and cancer
She needs data from other patients to compare and interpret Mabels DNA
She also has data available in her own lab, but she cannot share because of concerns how to deal with secure access to sensitive data and data governance, e.g. vetting of users
Further confounded by the data being highly fragmented.
Siloed in repositories and institutions around the world.
There are many public repositories, but It can be hugely confusing to know where to look for the right kind of data
The Repositive platform is an online community and marketplace connecting data consumers with data providers.
On Repositive, Jenn has
Easy, Interactive search
Faster data access workflow
Easy access to new data collaborators
Benefiting from reading feedback on data from community, colleagues, to assess data quality and utility
The Repositive platform and technology will remove barriers to data sharing and will incentivise users to explore, contribute and collaborate in alignment with best practices
The Repositive platform is an online community and marketplace connecting data consumers with data providers.
On Repositive, Jenn has
Easy, Interactive search
Faster data access workflow
Easy access to new data collaborators
Benefiting from reading feedback on data from community, colleagues, to assess data quality and utility
The Repositive platform and technology will remove barriers to data sharing and will incentivise users to explore, contribute and collaborate in alignment with best practices
The Repositive platform is an online community and marketplace connecting data consumers with data providers.
On Repositive, Jenn has
Easy, Interactive search
Faster data access workflow
Easy access to new data collaborators
Benefiting from reading feedback on data from community, colleagues, to assess data quality and utility
The Repositive platform and technology will remove barriers to data sharing and will incentivise users to explore, contribute and collaborate in alignment with best practices
The Repositive platform is an online community and marketplace connecting data consumers with data providers.
On Repositive, Jenn has
Easy, Interactive search
Faster data access workflow
Easy access to new data collaborators
Benefiting from reading feedback on data from community, colleagues, to assess data quality and utility
The Repositive platform and technology will remove barriers to data sharing and will incentivise users to explore, contribute and collaborate in alignment with best practices