The document discusses the concept of measuring impact in science. It notes that while scientists publish to record scientific findings, transfer information and knowledge, and gain credit, the notion of impact is complex and metrics like the Impact Factor, g-index, and h-index risk oversimplifying impact and turning academics into salespeople. Metrics are an imperfect way to measure scientific influence and risk rewarding sensationalism over quality work.
A Genome Sequence Analysis System Built with HypertableDATAVERSITY
Deep genome sequencing has revolutionized the fields of biology and medicine. Since January 2008, the capacity to generate sequence data has increased exponentially, far outpacing Moore's Law. The emergence of scalable NoSQL database technologies has made the analysis of this vast amount of sequence data not only feasible, but cost effective.
The University of California at San Francisco UCSF-Abbott Viral Detection and Discovery Center, led by director Charles Chiu, MD, PhD, Taylor Sittler, MD and the Hypertable development team have embarked upon a project to build a scalable software platform to facilitate deep sequencing analysis in diagnostic microbiology, transcriptomic analysis, and clinical / environmental metagenomics, areas for which existing commercial and academic solutions are sorely lacking. Doug Judd, the original creator of Hypertable, will present an overview of this genome sequencing analysis system. The presentation will cover the following topics:
Rationale for choosing NoSQL
Schema design
Sources and description of input data
Algorithms for generating and querying lookup tables
Table sizes and compression ratios
Lessons learned during system deployment
Recombinant adenoviruses provide a versatile system for gene expression studies and therapeutic applications in mammalian cells. There is no question that the adenovirus is the most effective means of delivering genes in vivo and in vitro. However construction of adenovirus vectors and virus packaging is time-consuming and labor intensive.
A Genome Sequence Analysis System Built with HypertableDATAVERSITY
Deep genome sequencing has revolutionized the fields of biology and medicine. Since January 2008, the capacity to generate sequence data has increased exponentially, far outpacing Moore's Law. The emergence of scalable NoSQL database technologies has made the analysis of this vast amount of sequence data not only feasible, but cost effective.
The University of California at San Francisco UCSF-Abbott Viral Detection and Discovery Center, led by director Charles Chiu, MD, PhD, Taylor Sittler, MD and the Hypertable development team have embarked upon a project to build a scalable software platform to facilitate deep sequencing analysis in diagnostic microbiology, transcriptomic analysis, and clinical / environmental metagenomics, areas for which existing commercial and academic solutions are sorely lacking. Doug Judd, the original creator of Hypertable, will present an overview of this genome sequencing analysis system. The presentation will cover the following topics:
Rationale for choosing NoSQL
Schema design
Sources and description of input data
Algorithms for generating and querying lookup tables
Table sizes and compression ratios
Lessons learned during system deployment
Recombinant adenoviruses provide a versatile system for gene expression studies and therapeutic applications in mammalian cells. There is no question that the adenovirus is the most effective means of delivering genes in vivo and in vitro. However construction of adenovirus vectors and virus packaging is time-consuming and labor intensive.
Dealing with scientific information 'overwhelm'. This slide set has been converted to ppt from Apple Keynote, and looks different from the original, especially the animations.
This seems better than the first upload.
Presentation on (semantic) nanopublications (specifically in biomedicine) given at iExpo in Paris, 10 June 2010. Partially in French (but mostly with English translation).
(in Apple Keynote 09)
Dealing with scientific information 'overwhelm'. This slide set has been converted to ppt from Apple Keynote, and looks different from the original, especially the animations.
These slides are from a talk given to the Fredericksburg Secular Humanists (FSH) in Fredericksburg, Virginia, on 8 November 2015. FSH is sub-chapter of the United Coalition of Reason (unitedcor.org). The talk compared the secular societies of the United States and Australia.
Odyssey Of The IWGSC Reference Genome Sequence: 12 Years 1 Month 28 Days 11 ...Fabio Caligaris
Presented at Plant Genomics and Gene Editing Congress: Europe. For more information visit: www.global-engage.com
To meet the challenges of sequencing the large, hexaploid genome, the IWGSC focused initially on developing a solid foundation for sequencing that would accommodate any future advancements in sequencing technologies: i.e., producing physical maps for all 21 individual bread wheat chromosomes.
vectorQC: 'A pipeline for assembling and annotation of vectors'Luca Cozzuto
DNA vectors are widely used in molecular cloning, gene engineering, studies of gene expression and other applications. Sequence validation of a vector DNA is a crucial quality control step before using the vector. With the cost of sequencing rapidly decreasing it becomes cost-effective to ensure the vectors quality using high-throughput sequencing and bioinformatics analysis. VectorQC is an automatic pipeline for quality control of a collection of sequenced DNA vectors. The pipeline is built using the NextFlow framework and is distributed with the Docker container, which makes the pipeline easy to install, modify, and re-use on any Unix-compatible OS on a computer, cluster or cloud
VS-CNV Annotations from the User's PerspectiveGolden Helix
Next-generation sequencing has enabled clinicians and researchers alike to identify novel genetic variants associated with rare Mendelian Diseases across the human genome. To help enable researchers and clinicians understand the role of CNVs in human health and disease, Golden Helix has a fully integrated CNV annotations to provide clinicians and researchers with more effective methods to identify pathogenic CNVs for heritable diseases. In this webcast, we will present our comprehensive clinical workflows that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants.
Analyzing Performance of the Twist Exome with CNV Backbone at Various Probe D...Golden Helix
Clinical Whole Exome Sequencing (WES) offers a high diagnostic yield test by detecting pathogenic variants in all coding genes of the human genome. WES is poised to consolidate multiple genetic tests by accurately identifying Copy Number Variation (CNV) events, typically necessitating microarray analyses. However, standard commercial exome kits are limited to targeting exon coding regions, leaving significant gaps in coverage between genes which could hinder comprehensive CNV detection.
Addressing the need for comprehensive coverage, Twist Bioscience has developed an enhanced Twist Exome 2.0 Plus Comprehensive Exome Spike-in capture panel with added "backbone" probes. These probes target common SNPs polymorphic in multiple populations and are evenly distributed in the intergenic and intronic regions, with three varying densities at 25kb, 50kb, and 100kb intervals. In this webcast, we discuss the combined efficacy of the backbone-probe enhanced exome capture kit and VS-CNV in identifying known CNVs using the Coriell CNVPANEL01 reference set.
This webcast reviews:
-The sensitivity rate for the detection of known CNV events at all three probe densities.
-The impact of best-practice quality metrics and filters on sensitivity.
-How VarSeq’s CNV annotation capabilities can be leveraged to identify likely pathogenic CNVs.
-The interpretation of clinically relevant CNVs using VSClinical.
Franz sterner tdwg 2016 new power balance needed for trustworthy biodiversity...taxonbytes
View a video recording here: https://vimeo.com/195024485
Franz & Sterner @ #TDWG16 - "A new power balance is needed for trustworthy biodiversity data". Talk # 1134, Friday, December 09, 2016, 11:30 am. Session Contributed Papers 05: Data Gaps, Trust, Knowledge Acquisition. See https://mbgserv18.mobot.org/ocs/index.php/tdwg/tdwg2016/schedConf/program
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.
Apollo and i5K: Collaborative Curation and Interactive Analysis of GenomesMonica Munoz-Torres
Precise elucidation of the many different biological features encoded in a genome requires a careful curation process that involves reviewing all available evidence to allow researchers to resolve discrepancies and validate automated gene models, protein alignments, and other biological elements. Genome annotation is an inherently collaborative task; researchers only rarely work in isolation, turning to colleagues for second opinions and insights from those with expertise in particular domains and gene families.
The i5k initiative seeks to sequence the genomes of 5,000 insect and related arthropod species. The selected species are known to be important to worldwide agriculture, food safety, medicine, and energy production as well as many used as models in biology, those most abundant in world ecosystems, and representatives in every branch of the insect phylogeny in an effort to better understand arthropod evolution and phylogeny. Because computational genome analysis remains an imperfect art, each of these new genomes sequenced will require visualization and curation.
Apollo is an instantaneous, collaborative, genome annotation editor, and the new JavaScript based version allows researchers real-time interactivity, breaking down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. The i5K is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process and Apollo is serving as the platform to empower this community. Here we offer details about this collaboration.
Dealing with scientific information 'overwhelm'. This slide set has been converted to ppt from Apple Keynote, and looks different from the original, especially the animations.
This seems better than the first upload.
Presentation on (semantic) nanopublications (specifically in biomedicine) given at iExpo in Paris, 10 June 2010. Partially in French (but mostly with English translation).
(in Apple Keynote 09)
Dealing with scientific information 'overwhelm'. This slide set has been converted to ppt from Apple Keynote, and looks different from the original, especially the animations.
These slides are from a talk given to the Fredericksburg Secular Humanists (FSH) in Fredericksburg, Virginia, on 8 November 2015. FSH is sub-chapter of the United Coalition of Reason (unitedcor.org). The talk compared the secular societies of the United States and Australia.
Odyssey Of The IWGSC Reference Genome Sequence: 12 Years 1 Month 28 Days 11 ...Fabio Caligaris
Presented at Plant Genomics and Gene Editing Congress: Europe. For more information visit: www.global-engage.com
To meet the challenges of sequencing the large, hexaploid genome, the IWGSC focused initially on developing a solid foundation for sequencing that would accommodate any future advancements in sequencing technologies: i.e., producing physical maps for all 21 individual bread wheat chromosomes.
vectorQC: 'A pipeline for assembling and annotation of vectors'Luca Cozzuto
DNA vectors are widely used in molecular cloning, gene engineering, studies of gene expression and other applications. Sequence validation of a vector DNA is a crucial quality control step before using the vector. With the cost of sequencing rapidly decreasing it becomes cost-effective to ensure the vectors quality using high-throughput sequencing and bioinformatics analysis. VectorQC is an automatic pipeline for quality control of a collection of sequenced DNA vectors. The pipeline is built using the NextFlow framework and is distributed with the Docker container, which makes the pipeline easy to install, modify, and re-use on any Unix-compatible OS on a computer, cluster or cloud
VS-CNV Annotations from the User's PerspectiveGolden Helix
Next-generation sequencing has enabled clinicians and researchers alike to identify novel genetic variants associated with rare Mendelian Diseases across the human genome. To help enable researchers and clinicians understand the role of CNVs in human health and disease, Golden Helix has a fully integrated CNV annotations to provide clinicians and researchers with more effective methods to identify pathogenic CNVs for heritable diseases. In this webcast, we will present our comprehensive clinical workflows that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants.
Analyzing Performance of the Twist Exome with CNV Backbone at Various Probe D...Golden Helix
Clinical Whole Exome Sequencing (WES) offers a high diagnostic yield test by detecting pathogenic variants in all coding genes of the human genome. WES is poised to consolidate multiple genetic tests by accurately identifying Copy Number Variation (CNV) events, typically necessitating microarray analyses. However, standard commercial exome kits are limited to targeting exon coding regions, leaving significant gaps in coverage between genes which could hinder comprehensive CNV detection.
Addressing the need for comprehensive coverage, Twist Bioscience has developed an enhanced Twist Exome 2.0 Plus Comprehensive Exome Spike-in capture panel with added "backbone" probes. These probes target common SNPs polymorphic in multiple populations and are evenly distributed in the intergenic and intronic regions, with three varying densities at 25kb, 50kb, and 100kb intervals. In this webcast, we discuss the combined efficacy of the backbone-probe enhanced exome capture kit and VS-CNV in identifying known CNVs using the Coriell CNVPANEL01 reference set.
This webcast reviews:
-The sensitivity rate for the detection of known CNV events at all three probe densities.
-The impact of best-practice quality metrics and filters on sensitivity.
-How VarSeq’s CNV annotation capabilities can be leveraged to identify likely pathogenic CNVs.
-The interpretation of clinically relevant CNVs using VSClinical.
Franz sterner tdwg 2016 new power balance needed for trustworthy biodiversity...taxonbytes
View a video recording here: https://vimeo.com/195024485
Franz & Sterner @ #TDWG16 - "A new power balance is needed for trustworthy biodiversity data". Talk # 1134, Friday, December 09, 2016, 11:30 am. Session Contributed Papers 05: Data Gaps, Trust, Knowledge Acquisition. See https://mbgserv18.mobot.org/ocs/index.php/tdwg/tdwg2016/schedConf/program
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.
Apollo and i5K: Collaborative Curation and Interactive Analysis of GenomesMonica Munoz-Torres
Precise elucidation of the many different biological features encoded in a genome requires a careful curation process that involves reviewing all available evidence to allow researchers to resolve discrepancies and validate automated gene models, protein alignments, and other biological elements. Genome annotation is an inherently collaborative task; researchers only rarely work in isolation, turning to colleagues for second opinions and insights from those with expertise in particular domains and gene families.
The i5k initiative seeks to sequence the genomes of 5,000 insect and related arthropod species. The selected species are known to be important to worldwide agriculture, food safety, medicine, and energy production as well as many used as models in biology, those most abundant in world ecosystems, and representatives in every branch of the insect phylogeny in an effort to better understand arthropod evolution and phylogeny. Because computational genome analysis remains an imperfect art, each of these new genomes sequenced will require visualization and curation.
Apollo is an instantaneous, collaborative, genome annotation editor, and the new JavaScript based version allows researchers real-time interactivity, breaking down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. The i5K is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process and Apollo is serving as the platform to empower this community. Here we offer details about this collaboration.
This is an introduction to a knowledge engineering methodology called 'Knowledge Engineering from Experimental Design' (KEfED). This methodology provides a powerful, intuitive method for modeling the design of scientific experiments and provides the foundation for work at the Biomedical Knowledge Engineering Group at the Information Sciences Institute (run by Gully Burns)
This presentation is a thorough guide to the use of Web Apollo, with details on User Navigation, Functionality, and the thought process behind manual annotation.
During this workshop, participants:
- Learn to identify homologs of known genes of interest in a newly sequenced genome.
- Become familiar with the environment and functionality of the Web Apollo genome annotation editing tool.
- Learn how to corroborate or modify automatically annotated gene models using available evidence in Web Apollo.
- Understand the process of curation in the context of genome annotation.
How SADI & SHARE help restore the Scientific Method to in silico scienceMark Wilkinson
This is my presentation to the Bio Open Source Convention (BOSC) in Boston, July 2010. I start with a brief status-update on the BioMoby project and then launch into a series of demonstrations of it's successor - SADI + SHARE. Rather than discussing how SADI/SHARE work, I focus the discussion on what role I think these technologies can play in bringing the traditional "scientific method" back into in silico biology.
Franz et al ice 2016 addressing the name meaning drift challenge in open ende...taxonbytes
Presentation for the Symposium: Building the Biodiversity Knowledge Graph for Insects – Components, Progress, and Challenges; 2016 XXV International Congress of Entomology, Orlando, FL – September 26, 2016 (#ICE2016). See https://esa.confex.com/esa/ice2016/meetingapp.cgi/Session/24482
The Semantic Web - This time... its PersonalMark Wilkinson
My presentation on SADI, SHARE, CardioSHARE, and the new iConsent project. Presented to the faculty and students at Stanford Medical Informatics, Palo Alto, USA. May 14th, 2010.
How do we make the semantic web, and medical research, more personal? (both for the researcher and for the patient) I present some ideas we're exploring
16. Herbert van de Sompel Johan Bollen
Michael Kurtz Peter Binfield Jevin West
Jorge Hirsch Jan Velterop Julia Lane
Alexis-Michel Mugabushaka
17.
18. growth of informal science communication
re-use of data as impact
metrics for data sets
measure
metrics suitable to take decisions? local metrics vs global ones
Eigenfactor vs Impact Factor web metrics poorly understood
h-bar index refinement of h-
focus on networks
index
multiple author, junior author, senior author
article level metrics relative funding decisions
increasing inputs not always leading to increased
output
how to quantify exposure in lay news
science is non-linear
media?
attributed nano-publications
24. Ascoviruses (AVs) induce a unique pathology in their insect host cells causing cleavage of the cells
into virion-containing vesicles. The mechanism by which AVs induce vesicle formation is poorly
understood. It is postulated that the virus initially induces apoptosis leading to cell fragmentation.
The apoptotic bodies are however, rescued by the virus to form the vesicles. Here we show that
Heliothis virescens AV (HvAV-3e) is able to inhibit chemically induced apoptosis from around 16 h
after infection. Analysis of the genome of the virus indicated the presence of a putative inhibitor of
apoptosis (orf28) gene that encodes a protein with an imperfect baculovirus inhibitor of apoptosis
repeat (BIR) and a RING domain. Transiently expressed orf28 did not inhibit chemically induced
apoptosis suggesting that the protein may not serve as an inhibitor of apoptosis. Nevertheless, RNA
interference studies revealed that the gene is probably essential for virus pathology and replication.
Ascoviruses
[16747851] Ascoviruses [16747851]
Induction
[26277419] Induction of Pathology [26277419
Pathology 13817745]
[13817745]
Insect [839958] Cell of Insect [283053 839958]
Cell [283053]
Ascoviruses > induction of pathology > insect cells
[16747851] > [26277419 13817745] > [283053 839958]
25. Ascoviruses (AVs) induce a unique pathology in their insect host cells causing cleavage of the cells
into virion-containing vesicles. The mechanism by which AVs induce vesicle formation is poorly
understood. It is postulated that the virus initially induces apoptosis leading to cell fragmentation.
The apoptotic bodies are however, rescued by the virus to form the vesicles. Here we show that
Heliothis virescens AV (HvAV-3e) is able to inhibit chemically induced apoptosis from around 16 h
after infection. Analysis of the genome of the virus indicated the presence of a putative inhibitor of
apoptosis (orf28) gene that encodes a protein with an imperfect baculovirus inhibitor of apoptosis
repeat (BIR) and a RING domain. Transiently expressed orf28 did not inhibit chemically induced
apoptosis suggesting that the protein may not serve as an inhibitor of apoptosis. Nevertheless, RNA
interference studies revealed that the gene is probably essential for virus pathology and replication.
Ascoviruses
[16747851] Ascoviruses [16747851]
Induction
[26277419] Induction of Pathology [26277419
Pathology 13817745]
[13817745]
Insect [839958] Cell of Insect [283053 839958]
Cell [283053]
Ascoviruses > induction of pathology > insect cells
[16747851] > [26277419 13817745] > [283053 839958]
Semantic codification of assertions
35. Credit in the ego-system; the acknowledge economy
Often seen as
impact
36.
37. “Scientific impact is the sound
you hear if you drop a feather
down the Grand Canyon and
wait for the echo.”
Paraphrasing Don Marquis, 1878-1937
38. “The notion of impact is incoherent, likely
to reward the sensationalist and second-
rate ... and risks turning academics into
door-to-door salesmen for vulgarised
versions of their increasingly market-
oriented products.”
Stefan Collini, professor of intellectual history and English
literature at the University of Cambridge
48. Apart from journal level , also article level metrics:
usage
citations
blog posts
bookmarks
comments/ratings
trackbacks
49. The less I understand it, the more
quality it is bound to have
50. The less I understand it, the more
quality it is bound to have
How about that as a metric?
51. Anyway, what does it mean, all these
metrics and the resulting ranking of
McJournals * and McArticles*?
52. Anyway, what does it mean, all these
metrics and the resulting ranking of
McJournals * and McArticles*?
* obviously, in this context ”Mc” just means:
falling within a narrow band of variability
55. Number of career decisions based purely on citation counts of one sort or another
56. Number of career decisions based purely on citation counts of one sort or another
57. Number of career decisions based purely on citation counts of one sort or another
Just in case this graph
makes it to the web – it’s
totally fictional!
58. Number of career decisions based purely on citation counts of one sort or another
Just in case this graph
makes it to the web – it’s
totally fictional!
But believable, too!
74. Julia Lane (NSF)
One thing that bugs me is that people answer the question ‘what
“ impact has your funding had’ with things like ‘I hired 3 postdocs and 2
support staff.’
”
Societal impact?
How has your research – done with our money – made the world a
better place?