Mary Ann Tuli's talk at the International Society of Biocuration meeting : What MODs can learn from Journals – a GigaDB curator’s perspective. Shanghai 9th April 2018
Federated Galaxy: Biomedical Computing at the FrontierEnis Afgan
Biomedical data exploration requires integrative analyses of large datasets using a diverse ecosystem of tools. For more than a decade, the Galaxy project (https://galaxyproject.org) has provided researchers with a web-based, user-friendly, scalable data analysis framework complemented by a rich ecosystem of tools (https://usegalaxy.org/toolshed) used to perform genomic, proteomic, metabolomic, and imaging experiments. Galaxy can be deployed on the cloud (https://launch.usegalaxy.org), institutional computing clusters, and personal computers, or readily used on a number of public servers (e.g., https://usegalaxy.org). In this paper, we present our plan and progress towards creating Galaxy-as-a-Service—a federation of distributed data and computing resources into a panoptic analysis platform. Users can leverage a pool of public and institutional resources, in addition to plugging-in their private resources, helping answer the challenge of resource divergence across various Galaxy instances and enabling seamless analysis of biomedical data.
Federated Galaxy: Biomedical Computing at the FrontierEnis Afgan
Biomedical data exploration requires integrative analyses of large datasets using a diverse ecosystem of tools. For more than a decade, the Galaxy project (https://galaxyproject.org) has provided researchers with a web-based, user-friendly, scalable data analysis framework complemented by a rich ecosystem of tools (https://usegalaxy.org/toolshed) used to perform genomic, proteomic, metabolomic, and imaging experiments. Galaxy can be deployed on the cloud (https://launch.usegalaxy.org), institutional computing clusters, and personal computers, or readily used on a number of public servers (e.g., https://usegalaxy.org). In this paper, we present our plan and progress towards creating Galaxy-as-a-Service—a federation of distributed data and computing resources into a panoptic analysis platform. Users can leverage a pool of public and institutional resources, in addition to plugging-in their private resources, helping answer the challenge of resource divergence across various Galaxy instances and enabling seamless analysis of biomedical data.
Data is the new asset class in the enterprise. Leveraging disk or cloud is just table stakes. Your data protection platform should make your data available where and when it needs to be available. This Webinar discusses what capabilities your data protection solution should provide.
Data Science deals with the extraction of valuable insights from an incredible number of sources in an endless number of formats. This session will go through a typical workflow using practical tools and tricks. This will give you a basic understanding of Data Science in the Cloud. The examples will show the steps that are needed to build and deploy a model to predict traffic collisions with weather data.
Jim discusses how Canada is currently positioned to take advantage of the data deluge, and how a range of stakeholders are involved in ongoing discussions to ensure Canada has the policies, infrastructure and tools to leverage this rich resource.
Open Access/Open Data Stocktaking–ILRI and Livestock CRP ILRI
Presented by Abenet Yabowork, Peter Ballantyne, Harrison Njamba, Jane Poole, Michael Victor at the CGIAR Data and Information Management Meeting Hyderabad, 14-15 October 2019
Basic concepts, best practices, pricing of using BigQuery the analytic data platform at petabyte scale from Google Cloud Platform. There is a lot things to learn about this tool and its features such as BI engine and AI Platform.
At Softroniics we provide job oriented training for freshers in IT sector. We are Pioneers in all leading technologies like Android, Java, .NET, PHP, Python, Embedded Systems, Matlab, NS2, VLSI etc. We are specializiling in technologies like Big Data, Cloud Computing, Internet Of Things (iOT), Data Mining, Networking, Information Security, Image Processing, Mechanical, Automobile automation and many other. We are providing long term and short term internship also.
We are providing short term in industrial training, internship and inplant training for Btech/Bsc/MCA/MTech students. Attached is the list of Topics for Mechanical, Automobile and Mechatronics areas.
MD MANIKANDAN-9037291113,04954021113
softroniics@gmail.com
Presented by Michael Victor, Abenet Yabowork, Jane Poole, Harrison Njamba, Erick Rutto and Peter Ballantyne at the ILRI open access week workshop, ILRI, Nairobi, 23-25 October 2019
ICRISAT Global Planning Meeting 2019: Research Data Management by Abhishek Ra...ICRISAT
ICRISAT has developed various data management and sharing platforms for better pedigree management, breeding practice analysis, survey management, climate prediction activities and the like, for better data management and to maximize the benefits of these research data as long term assets of ICRISAT and the global scientific community.
Pace of technology innovation, changes in publication, separating data generation from publishing insights. Given at the 2018 VIVO conference at Duke University.
Extended version of slides used for talk on "Scaling up (and doing business with) food safety information transparency" at the Food@Cranfield network (http://www.som.cranfield.ac.uk/som/p19207/research/research-clubs/food-cranfield-research-network), on an event dedicated to Using Big Data. Presented the concept of using AGINFRA to facilitate and scale up food safety data. Part of the Big Data Europe (http://www.big-data-europe.eu) liaison & dissemination activities.
Interactive and collaborative AI for biodiversity monitoring and beyond - JWK...SURFevents
ARISE is a platform for biodiversity research and AI evolution, built on open science principles to foster collaboration across institutes. We're developing an AI system to recognize all 8.7 million species on Earth, and envision our platform as a national infrastructure for open AI development. Our interactive AI training enables humans to annotate data while algorithms learn and select more meaningful data, optimizing time and improving performance.
Data is the new asset class in the enterprise. Leveraging disk or cloud is just table stakes. Your data protection platform should make your data available where and when it needs to be available. This Webinar discusses what capabilities your data protection solution should provide.
Data Science deals with the extraction of valuable insights from an incredible number of sources in an endless number of formats. This session will go through a typical workflow using practical tools and tricks. This will give you a basic understanding of Data Science in the Cloud. The examples will show the steps that are needed to build and deploy a model to predict traffic collisions with weather data.
Jim discusses how Canada is currently positioned to take advantage of the data deluge, and how a range of stakeholders are involved in ongoing discussions to ensure Canada has the policies, infrastructure and tools to leverage this rich resource.
Open Access/Open Data Stocktaking–ILRI and Livestock CRP ILRI
Presented by Abenet Yabowork, Peter Ballantyne, Harrison Njamba, Jane Poole, Michael Victor at the CGIAR Data and Information Management Meeting Hyderabad, 14-15 October 2019
Basic concepts, best practices, pricing of using BigQuery the analytic data platform at petabyte scale from Google Cloud Platform. There is a lot things to learn about this tool and its features such as BI engine and AI Platform.
At Softroniics we provide job oriented training for freshers in IT sector. We are Pioneers in all leading technologies like Android, Java, .NET, PHP, Python, Embedded Systems, Matlab, NS2, VLSI etc. We are specializiling in technologies like Big Data, Cloud Computing, Internet Of Things (iOT), Data Mining, Networking, Information Security, Image Processing, Mechanical, Automobile automation and many other. We are providing long term and short term internship also.
We are providing short term in industrial training, internship and inplant training for Btech/Bsc/MCA/MTech students. Attached is the list of Topics for Mechanical, Automobile and Mechatronics areas.
MD MANIKANDAN-9037291113,04954021113
softroniics@gmail.com
Presented by Michael Victor, Abenet Yabowork, Jane Poole, Harrison Njamba, Erick Rutto and Peter Ballantyne at the ILRI open access week workshop, ILRI, Nairobi, 23-25 October 2019
ICRISAT Global Planning Meeting 2019: Research Data Management by Abhishek Ra...ICRISAT
ICRISAT has developed various data management and sharing platforms for better pedigree management, breeding practice analysis, survey management, climate prediction activities and the like, for better data management and to maximize the benefits of these research data as long term assets of ICRISAT and the global scientific community.
Pace of technology innovation, changes in publication, separating data generation from publishing insights. Given at the 2018 VIVO conference at Duke University.
Extended version of slides used for talk on "Scaling up (and doing business with) food safety information transparency" at the Food@Cranfield network (http://www.som.cranfield.ac.uk/som/p19207/research/research-clubs/food-cranfield-research-network), on an event dedicated to Using Big Data. Presented the concept of using AGINFRA to facilitate and scale up food safety data. Part of the Big Data Europe (http://www.big-data-europe.eu) liaison & dissemination activities.
Interactive and collaborative AI for biodiversity monitoring and beyond - JWK...SURFevents
ARISE is a platform for biodiversity research and AI evolution, built on open science principles to foster collaboration across institutes. We're developing an AI system to recognize all 8.7 million species on Earth, and envision our platform as a national infrastructure for open AI development. Our interactive AI training enables humans to annotate data while algorithms learn and select more meaningful data, optimizing time and improving performance.
A description of BRISSKit, an open source tool that may be used to combine datasets held in different locations and analyse them for the purpose of research. Talk give by Jonathan Tedds of Leicester Uni. for the Data Management in Practice workshop, which took place on Nov 14th 2013 at the London School of Hygiene and Tropical Medicine
IDW2022: A decades experiences in transparent and interactive publication of ...GigaScience, BGI Hong Kong
Scott Edmunds at International Data Week 2022: A decades experiences in transparent and interactive publication of FAIR data and software via an end-to-end XML publishing platform. 21st June 2022
GigaByte Chief Editor Scott Edmunds presents on how to prepare a data paper for the TDR and WHO sponsored call for data papers describing datasets on vectors of human diseases launched in Nov 2021. Presented at the GBIF webinar on 25th January 2022 and aimed at authors interested in submitting a manuscript submitted to the series.
STM Week: Demonstrating bringing publications to life via an End-to-end XML p...GigaScience, BGI Hong Kong
Scott Edmunds at the STM Week 2020 Digital Publishing seminar on Demonstrating bringing publications to life via an End-to-end XML publishing platform. 2nd December 2020
Scott Edmunds: A new publishing workflow for rapid dissemination of genomes u...GigaScience, BGI Hong Kong
Scott Edmunds on a new publishing workflow for rapid dissemination of genomes using GigaByte & GigaDB. Presented at Biodiversity 2020 in the Annotation & Databases track, 9th October 2020.
Scott Edmunds: Quantifying how FAIR is Hong Kong: The Hong Kong Shareability ...GigaScience, BGI Hong Kong
Scot Edmunds talk at CODATA2019 on Quantifying how FAIR is Hong Kong: The Hong Kong Shareability of Hong Kong University Research Experiment. 19th September 2019 in Beijing
Scott Edmunds talk at IARC: How can we make science more trustworthy and FAIR...GigaScience, BGI Hong Kong
Scott Edmunds talk at IARC, Lyon. How can we make science more trustworthy and FAIR? Principled publishing for more evidence based research. 8th July 2019
PAGAsia19 - The Digitalization of Ruili Botanical Garden Project: Production...GigaScience, BGI Hong Kong
A 3 part talk presented at PAG Asia 2019 in Shenzhen- The Digitalization of Ruili Botanical Garden Project: Production, Curation and Re-Use. Presented by Huan Liu (CNGB), Scott Edmunds (GigaScience) & Stephen Tsui (CUHK). 8th June 2019
Democratising biodiversity and genomics research: open and citizen science to...GigaScience, BGI Hong Kong
Scott Edmunds at the China National GeneBank Youth Biodiversity MegaData Forum: Democratising biodiversity and genomics research: open and citizen science to build trust and fill the data gaps. 18th December 2018
Ricardo Wurmus at #ICG13: Reproducible genomics analysis pipelines with GNU Guix. Presented at the GigaScience Prize Track at the International Conference on Genomics, Shezhen 26th October 2018
Paul Pavlidis at #ICG13: Monitoring changes in the Gene Ontology and their im...GigaScience, BGI Hong Kong
Paul Pavlidis talk at the #ICG13 GigaScience Prize Track: Monitoring changes in the Gene Ontology and their impact on genomic data analysis (GOtrack). Shenzhen, 26th October 2018
Stefan Prost at #ICG13: Genome analyses show strong selection on coloration, ...GigaScience, BGI Hong Kong
Stefan Prost presentation for the #ICG13 GigaScience Prize Track: Genome analyses show strong selection on coloration, morphological and behavioral phenotypes in birds-of-paradise. Shenzhen, 26th October, 2018
Lisa Johnson at #ICG13: Re-assembly, quality evaluation, and annotation of 67...GigaScience, BGI Hong Kong
Lisa Johnson's talk at the #ICG13 GigaScience Prize Track: Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Shenzhen, 26th October 2018
Reproducible method and benchmarking publishing for the data (and evidence) d...GigaScience, BGI Hong Kong
Scott Edmunds presentation on: Reproducible method and benchmarking publishing for the data (and evidence) driven era. The Silk Road Forensics Conference, Yantai, 18th September 2018
Laurie Goodman: Sharing and Reusing Cell Image Data, ASCB/EMBO 2017 Subgroup ...GigaScience, BGI Hong Kong
Laurie Goodman's pre-prepared slides for the Subgroup S Sharing and Reusing Cell Image Data session at the 2017 ASCB│EMBO meeting in Philadelphia. December 2017
Susanna Sansone's talk at the "Beyond Open" Knowledge Dialogues/Open Data Hong Kong event on research data, hosted at the Hong Kong Innocentre on Monday 20 November 2017.
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.
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.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
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.
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.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
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.
Mammalian Pineal Body Structure and Also Functions
Mary Ann Tuli: What MODs can learn from Journals – a GigaDB curator’s perspective
1. What MODs can learn from Journals
– a GigaDB curator’s perspective
Mary Ann Tuli
9th April 2018
2. What is GigaDB
• GigaDB primarily serves as a repository to
host data and tools associated with articles in
GigaScience.
• GigaScience is an open access, open data,
open peer-review journal focusing on ‘big
data’ research from the life and biomedical
sciences.
7. The Growth of GigaDB
0
100
200
300
400
500
2011 2012 2013 2014 2015 2016 2017 2018
Total Datasets
20 different data
types, of which 60%
represent genomic
data, with software,
transcriptomic &
imaging datasets also
having high numbers.
8. New Developments
• 2 new curators (200% increase in staff!)
– Chris Armit – Data Scientist
• orcid 0000-0002-9952-8141
– Mary Ann Tuli – Data Editor
• orcid 0000-0002-4667-9528
– Join Chris Hunter – Lead Biocurator
• orcid 0000-0002-1335-0881
9. New Developments
• Imaging (Chris Armit)
– 3D model viewer
– CT and MRI images to be interactively explored
(see http://gigasciencejournal.com/blog/)
13. What I’ve learnt at GigaDB
• Authors are more invested
– Respond to queries (quickly!)
– Keen to work together
• Time pressures
14. “We need to make authors WANT to
make their data available”
Quote from a journal editor – ISB conference,
Cambridge 2013
15. What can the Biocurator Community
learn
• Better outreach
• Better personal communication
• Streamline submission pipelines
• What’s in it for them?
– Priority processing and availability in database
– Recognition
16. Giga Team
GigaScience won the 2018 Innovation in Journal
Publishing: Multidisciplinary Prose Award.
Editor-in-Chief Executive Editor Editors
Laurie Goodman Scott Edmunds Nicole Nogoy
Hans Zauner
Lead Data Manager Database Manager
Peter Li Si Zhe Xiao
Lead Biocurator Data Editor Data Scientist
Chris Hunter Mary Ann Tuli Chris Armit