Keynote talk to LEARN (LERU/H2020 project) for research data management. Emphasizes that problems are cultural not technical. Promotes modern approaches such as Git / continuousIntegration, announces DAT. Asserts that the Right to Read in the Right to Mine. Calls for widespread development of contentmining (TDM)
I CAN DO IT ALL BY MYSELF: : Exploring new roles for libraries and mediating ...Bohyun Kim
Presentation given at the American Library Association Annual Conference, Anaheim, CA. June 23, 2012.
Speaker: Bohyun Kim, Digital Access Librarian, Florida International University
Speaker: Jason Clark, Head of Digital Access and Web Services, Montana State University Libraries
Speaker: Patrick T. Colegrove, Head, DeLaMare Science & Engineering Library, University of Nevada, Reno
More program details: http://ala12.scheduler.ala.org/m/node/806
Open Data and Open Science presented in Rio for Open Science 2014-08-22. I argue that Open Notebook Science is the way forward and will lead to great benefits
Copyright is one of the greatest barrier to Open Data. This presentation for insidegovernment UK shows the struggle between those who want to reform copyright and those opposed to reform
Scientific information is often hidden or not published properly. The ContentMine is a Social Machine consisting of semantic software and communities of domain expertise; it aims to liberate all scientific facts from the published literature on a daily basis.
The talk , delivered to the Computational Institute, will be /was followed by a hands-on workshop learning how to use the technology and work as a community.
I CAN DO IT ALL BY MYSELF: : Exploring new roles for libraries and mediating ...Bohyun Kim
Presentation given at the American Library Association Annual Conference, Anaheim, CA. June 23, 2012.
Speaker: Bohyun Kim, Digital Access Librarian, Florida International University
Speaker: Jason Clark, Head of Digital Access and Web Services, Montana State University Libraries
Speaker: Patrick T. Colegrove, Head, DeLaMare Science & Engineering Library, University of Nevada, Reno
More program details: http://ala12.scheduler.ala.org/m/node/806
Open Data and Open Science presented in Rio for Open Science 2014-08-22. I argue that Open Notebook Science is the way forward and will lead to great benefits
Copyright is one of the greatest barrier to Open Data. This presentation for insidegovernment UK shows the struggle between those who want to reform copyright and those opposed to reform
Scientific information is often hidden or not published properly. The ContentMine is a Social Machine consisting of semantic software and communities of domain expertise; it aims to liberate all scientific facts from the published literature on a daily basis.
The talk , delivered to the Computational Institute, will be /was followed by a hands-on workshop learning how to use the technology and work as a community.
Published on Aug 22, 2014 by PMR
Open Data and Open Science presented in Rio for Open Science 2014-08-22. I argue that Open Notebook Science is the way forward and will lead to great benefits
Paradise Lost and The Right to Read is the Right to Minepetermurrayrust
Presented to UIUC CIRSS seminars to a mixed group of Library, CS, domain scientists with a great contingent of Early Career Researchers. Starts by honouring the creation of the wonderful NCSA Mosaic at UIUC in 1993 and the paradise of knowledge and community it opened. Then shows the gradual and tragic decline of the web into a megacorporate neocolonialist empire, where knowledge is sacrificed for money and power.
You have seen many of the slides before but the words are different and have been recorded.
contentmine.org (funded by Shuttleworth Foundation) has developed tools and workshops to allow anyone to mine scientific content. This 10-minute presentation at Wellcome Trust encourages you to become involved - no previous knowledge required.
Ethnography for impact: a new way of exploring user experience in librariesAndy Priestner
Presented by Andy Priestner at the SCONUL Winter Conference at the Royal College of Physicians on 21st November 2014.
A brief exploration of why librarians should be adopting ethnographic research methods in order to secure a more complete picture of user experience in their libraries. Incorporates details of three recent ethnographic research projects at Cambridge Judge Business School which have delivered many practical outcomes and directly impacted and improved service delivery.
What is Open Science / Open Research?; Initiative of the European Union (EU); Elements of Open Science: open research process / cycle; open access (open repositories); open data; open source software; open notebook / lab book; open workflows; open reputation systems; citizen science; relationship between open research and e-research; open science in Africa and South Africa
PhD Theses are normally locked away digitally. They cost 20 billion dollars to create and we waste much of this value. By making them open we can use software to read, index, reuse, compute and add massive value
Scholarly Publishing wastes huge amounts of valuable science. This presentation to the Public Library of Science suggests how we can work together to put this right
Published on Jul 10, 2015 by PMR
Scholarly Publishing wastes huge amounts of valuable science. This presentation to the Public Library of Science suggests how we can work together to put this right
Slides about LiquidPub project, presented at the 2nd Snow Workshop
http://wiki.liquidpub.org/mediawiki/index.php/Second_Workshop_on_Scientific_Knowledge_Creation%2C_Dissemination%2C_and_Evaluation
Vks Presentation, Jankowski,15 Jan2009, Websites & Books, Near FinalNick Jankowski
Network Venues & Scholarly Monographs:
Pioneering Initiatives in Publishing e-Scholarship
Abstract
Scholarly publishers are increasingly incorporating Web sites into facets of the enterprise. Often, such sites primarily serve basic promotional and purchasing functions, but occasionally sites of both publishers and authors reflect other functionalities: search facilities, availability of published text, referral to instructional and research materials, hyperlinks to external sources, opportunity for reader-author exchange. This presentation provides a panoramic overview of Web sites recently prepared by publishers and/or authors that complement traditionally published scholarly monograph. This overview is intended to stimulate discussion of suitable Web functionalities that might be incorporated into monograph publications being prepared by scholars affiliated to the Virtual Knowledge Studio.
Ontologies for baby animals and robots From "baby stuff" to the world of adul...Aaron Sloman
In contrast with ontology developers concerned with a symbolic or digital environment (e.g. the internet), I draw attention to some features of our 3-D spatio-temporal environment that challenge young humans and other intelligent animals and will also challenge future robots. Evolution provides most animals with an ontology that suffices for life, whereas some animals, including humans, also have mechanisms for substantive ontology extension based on results of interacting with the environment. Future human-like robots will also need this. Since pre-verbal human children and many intelligent non-human animals, including hunting mammals, nest-building birds and primates can interact, often creatively, with complex structures and processes in a 3-D environment, that suggests (a) that they use ontologies that include kinds of material (stuff), kinds of structure, kinds of relationship, kinds of process (some of which are process-fragments composed of bits of stuff changing their properties, structures or relationships), and kinds of causal interaction and (b) since they don't use a human communicative language they must use information encoded in some form that existed prior to human communicative languages both in our evolutionary history and in individual development. Since evolution could not have anticipated the ontologies required for all human cultures, including advanced scientific cultures, individuals must have ways of achieving substantive ontology extension. The research reported here aims mainly to develop requirements for explanatory designs. The attempt to develop forms of representation, mechanisms and architectures that meet those requirements will be a long term research project.
Using Social Media in Canadian Academic Libraries: A 2010 CARL ABRC Libraries...CARLsurvey2010
This is a survey of academic librarians working in Canada's research libraries (see CARL / ABRC libraries) and how they use social media. Your input will help Canada's major research libraries develop an understanding of what social media appears to offer academic librarians, and the challenges and issues of using it.
Use of ContentMine tools on the Open Access subset of EuropePubMedCentral to discover new knowledge about the Zika virus.
Three slides have embedded movies - these do not show in slideshare and a first pass of this can be seen as a single file at https://vimeo.com/154705161
Published on Aug 22, 2014 by PMR
Open Data and Open Science presented in Rio for Open Science 2014-08-22. I argue that Open Notebook Science is the way forward and will lead to great benefits
Paradise Lost and The Right to Read is the Right to Minepetermurrayrust
Presented to UIUC CIRSS seminars to a mixed group of Library, CS, domain scientists with a great contingent of Early Career Researchers. Starts by honouring the creation of the wonderful NCSA Mosaic at UIUC in 1993 and the paradise of knowledge and community it opened. Then shows the gradual and tragic decline of the web into a megacorporate neocolonialist empire, where knowledge is sacrificed for money and power.
You have seen many of the slides before but the words are different and have been recorded.
contentmine.org (funded by Shuttleworth Foundation) has developed tools and workshops to allow anyone to mine scientific content. This 10-minute presentation at Wellcome Trust encourages you to become involved - no previous knowledge required.
Ethnography for impact: a new way of exploring user experience in librariesAndy Priestner
Presented by Andy Priestner at the SCONUL Winter Conference at the Royal College of Physicians on 21st November 2014.
A brief exploration of why librarians should be adopting ethnographic research methods in order to secure a more complete picture of user experience in their libraries. Incorporates details of three recent ethnographic research projects at Cambridge Judge Business School which have delivered many practical outcomes and directly impacted and improved service delivery.
What is Open Science / Open Research?; Initiative of the European Union (EU); Elements of Open Science: open research process / cycle; open access (open repositories); open data; open source software; open notebook / lab book; open workflows; open reputation systems; citizen science; relationship between open research and e-research; open science in Africa and South Africa
PhD Theses are normally locked away digitally. They cost 20 billion dollars to create and we waste much of this value. By making them open we can use software to read, index, reuse, compute and add massive value
Scholarly Publishing wastes huge amounts of valuable science. This presentation to the Public Library of Science suggests how we can work together to put this right
Published on Jul 10, 2015 by PMR
Scholarly Publishing wastes huge amounts of valuable science. This presentation to the Public Library of Science suggests how we can work together to put this right
Slides about LiquidPub project, presented at the 2nd Snow Workshop
http://wiki.liquidpub.org/mediawiki/index.php/Second_Workshop_on_Scientific_Knowledge_Creation%2C_Dissemination%2C_and_Evaluation
Vks Presentation, Jankowski,15 Jan2009, Websites & Books, Near FinalNick Jankowski
Network Venues & Scholarly Monographs:
Pioneering Initiatives in Publishing e-Scholarship
Abstract
Scholarly publishers are increasingly incorporating Web sites into facets of the enterprise. Often, such sites primarily serve basic promotional and purchasing functions, but occasionally sites of both publishers and authors reflect other functionalities: search facilities, availability of published text, referral to instructional and research materials, hyperlinks to external sources, opportunity for reader-author exchange. This presentation provides a panoramic overview of Web sites recently prepared by publishers and/or authors that complement traditionally published scholarly monograph. This overview is intended to stimulate discussion of suitable Web functionalities that might be incorporated into monograph publications being prepared by scholars affiliated to the Virtual Knowledge Studio.
Ontologies for baby animals and robots From "baby stuff" to the world of adul...Aaron Sloman
In contrast with ontology developers concerned with a symbolic or digital environment (e.g. the internet), I draw attention to some features of our 3-D spatio-temporal environment that challenge young humans and other intelligent animals and will also challenge future robots. Evolution provides most animals with an ontology that suffices for life, whereas some animals, including humans, also have mechanisms for substantive ontology extension based on results of interacting with the environment. Future human-like robots will also need this. Since pre-verbal human children and many intelligent non-human animals, including hunting mammals, nest-building birds and primates can interact, often creatively, with complex structures and processes in a 3-D environment, that suggests (a) that they use ontologies that include kinds of material (stuff), kinds of structure, kinds of relationship, kinds of process (some of which are process-fragments composed of bits of stuff changing their properties, structures or relationships), and kinds of causal interaction and (b) since they don't use a human communicative language they must use information encoded in some form that existed prior to human communicative languages both in our evolutionary history and in individual development. Since evolution could not have anticipated the ontologies required for all human cultures, including advanced scientific cultures, individuals must have ways of achieving substantive ontology extension. The research reported here aims mainly to develop requirements for explanatory designs. The attempt to develop forms of representation, mechanisms and architectures that meet those requirements will be a long term research project.
Using Social Media in Canadian Academic Libraries: A 2010 CARL ABRC Libraries...CARLsurvey2010
This is a survey of academic librarians working in Canada's research libraries (see CARL / ABRC libraries) and how they use social media. Your input will help Canada's major research libraries develop an understanding of what social media appears to offer academic librarians, and the challenges and issues of using it.
Use of ContentMine tools on the Open Access subset of EuropePubMedCentral to discover new knowledge about the Zika virus.
Three slides have embedded movies - these do not show in slideshare and a first pass of this can be seen as a single file at https://vimeo.com/154705161
Talk to OpenForum Academy (Open Forum Europe) about Text and data Mining. Four use cases selected fo non-scientists. Also discussion of latest on Europena copyright reform and TDM exceptions
A Global Commons for Scientific Data: Molecules and Wikidatapetermurrayrust
Methods for extracting facts from the scientific literature, and linking them to Wikidata IDs. Wikidata is introduced by an architectural example and bioscience. Then we explore how data can be extracted from text and from images
High throughput mining of the scholarly literature; talk at NIHpetermurrayrust
The scientific and medical literature contains huge amounts of valuable unused information. This talk shows how to discover it, extract, re-use and interpret it. Wikidata is presented as a key new tool and infrastructure. Everyone can become involved. However some of the barriers to use are sociopolitical and these are identified and discussed.
High throughput mining of the plant-science literaturepetermurrayrust
We can now mine the plant science literature for facts, especially species (both plants and others), chemicals, diseases and other agricultural terms. This presentation gives a number of examples and links on how you can do this on the Open Access literature
Amanuens.is HUmans and machines annotating scholarly literaturepetermurrayrust
about 10,000 scholarly articles ("papers") are published each day. Amanuens.is is a symbiont of ContentMine and Hypothes.is (both Shuttleworth projects/Fellows) which annotates theses using an array of controlled vocabularies ("dictionaries"). The results, in semantic form are used to annotate the original material. The talk had live demos and used plant chemistry as the examples
Automatic Extraction of Knowledge from Biomedical literaturepetermurrayrust
a plenary lecture to Cochrane Collaboration in Birmingham, on the value of automatically extracting knowledge. Covers the Why? How? What? Who? and problems and invites collaboration
ContentMining for France and Europe; Lessons from 2 years in UKpetermurrayrust
I have spend 2 years carrying out Content Mining (aka Text and Data Mining) in the UK under the 2014 "Hargreaves" exception. This talk was given in Paris, to ADBU , after France had passed the law of the numeric Republique. I illustrate what worked in what did not and why and offer ideas to France and Europe
Published on Jan 29, 2016 by PMR
Keynote talk to LEARN (LERU/H2020 project) for research data management. Emphasizes that problems are cultural not technical. Promotes modern approaches such as Git / continuous Integration, announces DAT. Asserts that the Right to Read in the Right to Mine. Calls for widespread development of content mining (TDM)
The Culture of Research Data, by Peter Murray-RustLEARN Project
1st LEARN Workshop. Embedding Research Data as part of the research cycle. 29 Jan 2016. Presentation by Peter Murray-Rust, ContentMine.org and University of Cambridge
Early Career Reseachers in Science. Start Early, Be Open , Be Bravepetermurrayrust
Highlights the importance of supporting Early Career Researchers to pursue their own ideas, possibly alongside their main research. Illustrated with biology but applies to all fields of science. This was a 14 min presentation and shows narratives of how ECRs develop and reinforce each other.
Presentation given at NUI, Galway 2019-04-11 for Open Science Week.
An overview of Early Career Researchers, their innovation and contribution towards Open Infrastructure
The ContentMine system (Open Source) can search EuropePMC and download hundreds of articles in seconds. These can be indexed by AMI dictionaries allowing a rapid evaluations and refinement of the search
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
Slides describing Force11 Work and background of several of the speakers, used for talks to University of Lethbridge, Carnegie Mellon and to Elsevier internally
The Evolution of e-Research: Machines, Methods and MusicDavid De Roure
David De Roure's Inaugural Lecture on 28th October at Oxford e-Research Centre, University of Oxford, UK
10 years ago we saw a few early adopters of e-Science technology; now we see acceleration of research through broader adoption and sharing of tools, techniques and artefacts, both for 'big science' and the 'long tail scientist'.
Will this incremental trend continue or are we seeing glimpses of a phase change ahead, where researchers harness these emerging digital capabilities to address research questions in ways that simply were not possible before?
This talk will describe three generations of e-Research, using the myExperiment social website as a lens to glimpse future research practice, and focusing on a web-scale computational musicology project as an illustration of 3rd generation thinking.
Also available from http://wiki.myexperiment.org/index.php/Presentations
Automatic Extraction of Science and Medicine from the scholarly literatureTheContentMine
Published on Jun 04, 2015 by PMR
Many scientists have to extract many facts out the scholarly literature - to evaluate other work or to extract useful collections of facts. This shows the approach, especially for systematic reviews of animal or clinical trials
Automatic Extraction of Science and Medicine from the scholarly literaturepetermurrayrust
Many scientists have to extract many facts out the scholarly literature - to evaluate other work or to extract useful collections of facts. This shows the approach, especially for systematic reviews of animal or clinical trials
The scientific scholarly literature now contains many millions of articles. The contain semi-structured information of high quality and veracity. We show how this resource can be converted to a universal Wikicite format and full-text indexed against Wikidata dictionaries. We now have > 5 million bibliographic records and over 200 dictionaries based in Wikidata properties and queriable by SPARQL.
Talk to EBI Industry group on Open Software for chemical and pharmaceutical sciences. Covers examples of chemistry , wit demos, and argues that all public knowledge should be Openly accessible
Published on May 18, 2016 by PMR
Talk to EBI Industry group on Open Software for chemical and pharmaceutical sciences. Covers examples of chemistry , wit demos, and argues that all public knowledge should be Openly accessible
Jean-Claude Bradley presents on "Peer Review and Science2.0: blogs, wikis and social networking sites" as a guest lecturer for the “Peer Review Culture in Scholarly Publication and Grantmaking” course at Drexel University. The main thrust of the presentation is that peer review alone is not capable of coping with the increasing flood of scientific information being generated and shared. Arguments are made to show that providing sufficient proof for scientific findings does scale and weakens the tragedy of the trusted source cascade.
Can machines understand the scientific literature?petermurrayrust
A presentation to Cambridge MPhil Computational Biology. 2020-11-11 . Presenters Peter Murray-Rust, Shweata Hegde and Ambreen Hamadani from https://github.com/petermr/openvirus .
This chunk is PMR with a large break in the middle for SH and AH talks.
I cover Global Challenges, knowledge equity, semantics of scientific articles, Wikidata, Data Extraction from images, and ethics/politics.
Answer: Yes, technically. No, politically as the Publisher-Academic Complex will block it.
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.
Overview of openVirus project. Interns in India have worked for 2 months to extract scientific knowledge from the literature about viral epidemics. Covers data science, machine learning and virtual collaboration
Automatic mining of data from materials science literaturepetermurrayrust
The literature on materials science (batteries, etc.) contains huge amounts of scientific facts, but not in easily accessible form. our AMI program has been developed to automatically:
scrape , clean, annotate and display/publish
data for re-use in science.
Examples will be given from electrochemistry, magnetism and other fields . The general principles and (open) tech are applicable to many other disciplines.
A presentation by Open Climate Knowledge for European Forum for Advanced Practices. Showing how the scientific literature can be searched for knowledge on this multidisciplinary topic.
XML for science; its huge potential; but are pubiishers preventing it?petermurrayrust
XML can represent almost all well derfined scientific objects. chemistry, plants medcine. But it's not yet widely used. Is this because publishers oppose thr re-use of science?
The scientific and medical literature is a vast resource of knowledge, but it needs turning into semantic FAIR form. The ContentMine can do this and we presented a rapid overview of the potential
A 10-minute talk to lovers of early science (e.g. 1600-1900) at the Royal Society. Archivists , computer vision, scientific historical metadata all relevant.
I chose 4 examples of monochrome diagrams that I can extract something from automatically. Some of the methids would scale to larger volumes , e.g. tables for figures, or maps with points
WikiFactMine: Ontology for Everybody and Everythingpetermurrayrust
WikiFactMine https://www.wikidata.org/wiki/Wikidata:WikiFactMine consists of several hundreds dictionaries created from Wikidata. They cover everything from science to medicine to geo to arts. Every item has a unique identifier (Q) and normally has several properties (P) creating a series of triples. Using SPARQL it's possible to create sophiticated queries and run them in seconds
The Publisher -Academic complex is a dystopian cycle where academia gives (mega)publishers manuscripts, reviews and money and the publishers give personal and institutional glory(vanity). This is analysed in its origins, impact and harm. The disruption can come from Advocacy/Activism, Community and Tools. Disruption comes from doing things Better or Novel, not Prices
AUDIO : https://soundcloud.com/damahub/peter-murray-rust-disturbing-the-publisher-academic-complex-210418-british-library
Thanks to DaMaHub
This has now been edited by Ewan McAndrew (Edinburgh Wikimedian in Residence) many thanks - to synchronize the slides with the soundtrack. https://media.ed.ac.uk/media/1_46h85ltt Brilliant
ContentMining (aka Text and Data Mining TDM) is beneficial, legal in the UK and a few other countries. Many groups in Europe are looking to make it legal there as well but there are many vested interests who oppose it.
This short presentation shows the benefits of content mining, some of the technology, and the way that it can be used and promotedby communities of practice. I urge all attendees at CopyCamp and also the wider world to press for liberalization of Copyright
The mining "Revolution"; are Libraries supporting Researchers or Publishers"?petermurrayrust
increasingly we find that mega-corporations have taken control over scholarship. We could use the scholarly literature as a knowledge resource but megacorps try to stop this - and often libraries support them rather than researchers.
WikiFactMine uses dictionaries created directly from Wikidata to search the scientific literature. The example given is for papers which contain mention of conifers and terpenes (volatile plant organic compounds). Traditional queries and content are expanded by the system to be much broader and more precise than traditional keyword searchers of abstract
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
PRESENTATION ABOUT PRINCIPLE OF COSMATIC EVALUATION
The culture of researchData
1. The Culture of Research Data
Peter Murray-Rust,
ContentMine.org and UniversityOfCambridge
LEARN, London, UK 2016-01-29
The technology for Managing Research Data is already here…
…but we need a change of culture
Open Notebook Science
Publishers must be forced to serve us, not control us
2. Just read the big
letters
He’s got zillions of
slides…
4. The Right to Read is the Right to Mine
http://contentmine.org
5. Themes
• Highly domain-dependent (chem, cryst, phylo)
• Requires community and centrality
• University repositories are NOT the solution
• Openness makes it dramatically easier/better
• The publisher-academic complex is a major
problem.
• Infrastructure must be open and under our
control
6. WE pay for scholarly
publications that WE
can’t read
[1] The Military-Industrial-Academic complex (1961)
(Dwight D Eisenhower, US President)
Publishers Academia
Glory+?
$$, MS
review
Taxpayer
Student
Researcher
$$ $$
in-kind
The Publisher-Academic complex[1]
8. Some topics
• Github / software mgt informs data mgt
• Open notebook science
• Open source malaria + LabTrove
• Open phylogenetics
• Computational chemistry
• Crystallography
• Early career researchers can change the world, if
we support them.
• ContentMining (TDM) as research
• Are “publishers” tyrants or servants?
10. Why I reposit software in GitHub
I WANT TO!!!
BETTER
QUICKER
SECURE
AUDIT
BACKTRACKABLE
EASY
get collaborators
Most early career software creators have repos
How many people have USED Git?
14. Compile Fail
Inactive
Fail Tests
Pass Tests
Continuous Integration (Jenkins)
Every time I commit a change
50 projects are recompiled
and tested.
Impossible to do this manually!
16. Traditional Research and Publication
“Lab” work paper/th
esis
Write
rewrite
Re-experiment
publish
???
Validation??
DATA
output “belongs”
to publisher
Every process is LOSSY
17. How NOT to publish data
HT Henry Rzepa
From Henry Rzepa:
this article http://doi.org/10.1126/science.aad6252
which provides a 22 Mbyte PDF of data (mostly bitmaps of NMR
spectra) and comes in at 404 pages long. [1]
But this one http://doi.org/10.1021/jacs.5b05902 [comp chem]
is 505 pages long (the current record holder?)
[1] DATA Behind paywall
18. 505 pages PDF, was a
machine-readable log file
that could and
should have been in a repo
Computational
Chemistry
19. MORE of the PDF
DATA Destruction
Blind humans and
Machines cannot
read this
22. JD Bernal’s 1965 vision
However large an array of facts, however rapidly they
accumulate, it is possible to keep them in order and to
extract from time to time digests containing the most
generally significant information, while indicating how to
find those items of specialized interest. To do so, however,
requires the will and the means. (Bernal, 1965)
Quoted by PMR in http://journals.iucr.org/d/issues/1998/06/01/ba0011/ba0011.pdf
24. https://en.wikipedia.org/wiki/Bermuda_Principles
• Automatic release of sequence assemblies larger than 1
kb (preferably within 24 hours).
• Immediate publication of finished annotated
sequences.
• Aim to make the entire sequence freely available in the
public domain for both research and development in
order to maximise benefits to society.
HUMAN GENOME project used
Open Notebooks
Without
29. Mat Todd (Sydney) and MANY collaborators
http://opensourcemalaria.org/ (Chrome for interactivity)
Mat Todd, Univ Sydney, runs an Open Notebook community
to create new antimalarials.
35. data is associated with the proposed
scientific endeavour prior to or at the
point of creation rather than by
annotating the data with commentary
after the experiment has taken place
University of Southampton
37. Henry Rzepa does Open
Notebook Computational
Chemistry…
http://www.rzepa.net/blog/?p=14272
This is a current open notebook discussion,
http://www.ch.imperial.ac.uk/rzepa/blog/?p=15552 (see comments,
currently 67).
… on his blog
41. Crystallography – a model for Data
Management
• Pro-active, friendly international community
• Committed active International Union(IUCr)
• Data publication valued (1960-present)
• Community develops semantics/dictionaries
• Committed volunteer software innovators
• Heavily Open approach
• Massive and valuable re-use of data
• Culture of validation/reproducibility
• Respect and credit for tool development
46. Where to reposit published
crystallography?
Proteins -> PDB, Open
BUT
Inorganics -> ICSD Closed
Organics -> Cambridge (CCDC) Closed
SO
The community has built a Crystallography Open
Database
47. Restrictions on Re-use of Crystallographic data
NOTE: The CCDC is based on data contributed by
scientists as part of publication and validation
Crystallographic data from
publications now belongs to CCDC
54. Rotation-Based Learning (RBL)
Phase 1: Initiator
• No communication
permitted between groups
• Attempt to reproduce
existing literature
• Deliver a coherent research
story by the end of Phase 1
Phase 2: Successor
• Communication between
groups still prohibited
• Validate and develop the
inherited research story
• Critique your predecessors
• Role of research producer vs. research user
• Can this approach help to foster awareness of reproducibility issues?
Throughout Phases 1 & 2:
• Daily lectures on open
science culture & techniques
• First-hand application to own
research work
• Version control using GitHub
• Daily group supervision
56. So we can now
legally contentmine
the whole literature
in the UK…
NORMA
Ross Mounce and PMR
created a SuperTree of Life
for microorganisms!
…Yes! And in UK
we are starting
to do it…
70. The John S. and James L. Knight Foundation is an American private, non-profit foundation
dedicated to supporting "transformational ideas that promote quality journalism, advance
media innovation, engage communities and foster the arts."[2]
DAT supports public data
71. @Senficon (Julia Reda) :Text & Data mining in times of
#copyright maximalism:
"Elsevier stopped me doing my research"
http://onsnetwork.org/chartgerink/2015/11/16/elsevi
er-stopped-me-doing-my-research/ … #opencon #TDM
Elsevier stopped me doing my research
Chris Hartgerink
72. I am a statistician interested in detecting potentially problematic research such as data fabrication,
which results in unreliable findings and can harm policy-making, confound funding decisions, and
hampers research progress.
To this end, I am content mining results reported in the psychology literature. Content mining the
literature is a valuable avenue of investigating research questions with innovative methods. For
example, our research group has written an automated program to mine research papers for errors in
the reported results and found that 1/8 papers (of 30,000) contains at least one result that could
directly influence the substantive conclusion [1].
In new research, I am trying to extract test results, figures, tables, and other information reported in
papers throughout the majority of the psychology literature. As such, I need the research papers
published in psychology that I can mine for these data. To this end, I started ‘bulk’ downloading research
papers from, for instance, Sciencedirect. I was doing this for scholarly purposes and took into account
potential server load by limiting the amount of papers I downloaded per minute to 9. I had no intention
to redistribute the downloaded materials, had legal access to them because my university pays a
subscription, and I only wanted to extract facts from these papers.
Full disclosure, I downloaded approximately 30GB of data from Sciencedirect in approximately 10 days.
This boils down to a server load of 0.0021GB/[min], 0.125GB/h, 3GB/day.
Approximately two weeks after I started downloading psychology research papers, Elsevier notified my
university that this was a violation of the access contract, that this could be considered stealing of
content, and that they wanted it to stop. My librarian explicitly instructed me to stop downloading
(which I did immediately), otherwise Elsevier would cut all access to Sciencedirect for my university.
I am now not able to mine a substantial part of the literature, and because of this Elsevier is directly
hampering me in my research.
[1] Nuijten, M. B., Hartgerink, C. H. J., van Assen, M. A. L. M., Epskamp, S., & Wicherts, J. M. (2015). The
prevalence of statistical reporting errors in psychology (1985–2013). Behavior Research Methods, 1–22.
doi: 10.3758/s13428-015-0664-2
Chris Hartgerink’s blog post
73. Some Children
of the Digital Enlightenment
• David Carroll & Joe McArthur: OAButton
• Rayna Stamboliyska & Pierre-Carl Langlais
• Jon Tennant
• Ross Mounce
• Jenny Molloy
• Erin McKiernan
• Jack Andraka
• Michelle Brook
• Heather Piwowar
• TheContentMine Team
• Rufus Pollock
• Jonathan Gray
• Sophie Kay
Jean-Claude Bradley [1] a chemist
developed Open notebook science;
making the entire primary record of a
research project publicly available
online as it is recorded. (WP)
J-C promoted these ideas with
UNDERGRADUATE scientists.
[1] Unfortunately J-C died in 2014;
we held a memorial meeting in
Cambridge
Sophie
Kay
78. This is a current open notebook discussion, http://www.ch.imperial.ac.uk/rzepa/blog/?p=15552
(see comments, currently 67).
This is an earlier one, http://www.rzepa.net/blog/?p=14272 (with 86 comments) and also
incorporates Jsmol to visualise all the data
This one starts discussion as an open notebook http://www.ch.imperial.ac.uk/rzepa/blog/?p=1211
with the resulting formal publication at 10.1002/jcc.23985
This was the original open notebook post http://www.ch.imperial.ac.uk/rzepa/blog/?p=984 with
the resulting formal publication at 10.1038/NCHEM.596
This one incorporates open data into its citation list
http://www.ch.imperial.ac.uk/rzepa/blog/?p=15505 and is also an open notebook follow up to my
PhD thesis work, formally published in 1975 or so, thus operating in reverse to the above.
This shows some end outcomes: http://www.ch.imperial.ac.uk/rzepa/blog/?p=15313
This shows the principles: http://www.ch.imperial.ac.uk/rzepa/blog/?p=10972
This is an introductory tutorial http://www.ch.imperial.ac.uk/rzepa/blog/?p=14454
This is a critique http://www.ch.imperial.ac.uk/rzepa/blog/?p=13826
This is “convincing case” http://www.ch.imperial.ac.uk/rzepa/blog/?p=13248
This is about metadata http://www.ch.imperial.ac.uk/rzepa/blog/?p=12932
And its use http://www.ch.imperial.ac.uk/rzepa/blog/?p=12526
You have seen this data nightmare before: http://www.ch.imperial.ac.uk/rzepa/blog/?p=12728
This is about ORCID http://www.ch.imperial.ac.uk/rzepa/blog/?p=12513
86. Ross Mounce (Bath), Panton Fellow
• Sharing research data:
http://www.slideshare.net/rossmounce
• How-to figures from PLOS/One [link]:
Ross shows how to bring figures to life:
• PLOSOne at http://bit.ly/PLOStrees
• PLOS at http://bit.ly/phylofigs (demo)
Editor's Notes
Hi, I’m here to talk about AMI; a data extraction framework and tool. First, I just want highlight some of key contributors to the projects; Andy for his work on the ChemistryVisitor and Peter for the overall architecture.
In this talk, I’m going to impress the importance of data in a specific format and its utility to automated machine processing. Then I’m going to demonstrate AMI’s architecture and the transformation of data as it flows through the process. I’m going to dwell a little on a core format used, Scalable Vector Graphics (SVG) before introducing the concept of visitors, which are pluggable context specific data extractors. Next, I’m going to introduce Andy’s ChemVisitor, for extracting semantic chemistry data, along with a few other visitors that can process non-chemistry specific data. Finally, I will demonstrate some uses of the ChemVisitor, within the realm of validation and metabolism.