The document summarizes an upcoming Biological Visualization community meetup taking place on November 10, 2014 in Paris, France. It outlines the agenda and plans to discuss community activities and events for 2014-2016, including BioVis conferences, the VIZBI and VCBM meetings, and establishing a Biological Visualization community organization. Details are provided on dates, locations, deadlines and topics for many of these events.
There is an overwhelming number of new resources for chemistry that would likely benefit both librarians and students in terms of improving access to data and information. While commercial solutions provided by an institution may be the primary resources there is now an enormous range of online tools, databases, resources, apps for mobile devices and, increasingly, wikis. This presentation will provide an overview of how wiki-based resources for scientists are developing and will introduce a number of developing wikis. These include wikis that are being used to teach chemistry to students as well as to source information about scientists, scientific databases and mobile apps.
There is an overwhelming number of new resources for chemistry that would likely benefit both librarians and students in terms of improving access to data and information. While commercial solutions provided by an institution may be the primary resources there is now an enormous range of online tools, databases, resources, apps for mobile devices and, increasingly, wikis. This presentation will provide an overview of how wiki-based resources for scientists are developing and will introduce a number of developing wikis. These include wikis that are being used to teach chemistry to students as well as to source information about scientists, scientific databases and mobile apps.
ELIXIR Pilot Actions launched in 2014: Integration of BILS-ProteomeXchange us...Juan Antonio Vizcaino
This is a report of the ELIXIR pilot project performed by the EMBL-EBI (PRIDE and System teams), BILS and EUDAT. The title of the pilot project was: "Integration of BILS-ProteomeXchange using EUDAT resources".
Supporting open research - how to help your researchers - Vitae15Kevin Ashley
A talk given at a Vitae event in Leeds, 2015-12-01, on how universities and other research organisations can help their researchers practice open research, with a special focus on the training resources provided by FOSTER.
There is an overwhelming number of new resources for chemistry that would likely benefit both librarians and students in terms of improving access to data and information. While commercial solutions provided by an institution may be the primary resources there is now an enormous range of online tools, databases, resources, apps for mobile devices and, increasingly, wikis. This presentation will provide an overview of how wiki-based resources for scientists are developing and will introduce a number of developing wikis. These include wikis that are being used to teach chemistry to students as well as to source information about scientists, scientific databases and mobile apps.
There is an overwhelming number of new resources for chemistry that would likely benefit both librarians and students in terms of improving access to data and information. While commercial solutions provided by an institution may be the primary resources there is now an enormous range of online tools, databases, resources, apps for mobile devices and, increasingly, wikis. This presentation will provide an overview of how wiki-based resources for scientists are developing and will introduce a number of developing wikis. These include wikis that are being used to teach chemistry to students as well as to source information about scientists, scientific databases and mobile apps.
ELIXIR Pilot Actions launched in 2014: Integration of BILS-ProteomeXchange us...Juan Antonio Vizcaino
This is a report of the ELIXIR pilot project performed by the EMBL-EBI (PRIDE and System teams), BILS and EUDAT. The title of the pilot project was: "Integration of BILS-ProteomeXchange using EUDAT resources".
Supporting open research - how to help your researchers - Vitae15Kevin Ashley
A talk given at a Vitae event in Leeds, 2015-12-01, on how universities and other research organisations can help their researchers practice open research, with a special focus on the training resources provided by FOSTER.
Slides for a workshop session on "Building an Accessible Digital Institution" facilitated by Brian Kelly, Innovation Advocate, Cetis at the Cetis conference held at the University of Bolton on 17-18 June 2014.
See http://www.slideshare.net/Thebriankelly/building-an-accessible-digital-institution
Presentation to meeting, Heraklion, 4th June 2014 on constructing a marine virtual laboratory from the bottom up in the context of LifeWatch. Covers:
- Constructing LifeWatch – reminders of what we are doing
- Sourcing the right ingredients - The “Service Network” idea
- Steps towards building Virtual Laboratories.
Intro to GBIF: Infrastructures and Platforms for Environmental Crowd Sensing ...Kyle Copas
Slides presented while representing GBIF—the Global Biodiversity Information Facility (http://gbif.org)—at 'Infrastructures and Platforms for Environmental Crowd Sensing and Big Data' at the European Environment Agency on 9 Sept 2015. The session was part of EnviroInfo and ICT for Sustainability, a three-day conference in Copenhagen hosted by the University of Copenhagen in collaboration with the European Environment Agency.
Points of discussion for the steering group meeting, update on Kaptur etc. Presentation on the overall findings of the Environmental Assessment, by Marie-Therese Gramstadt, Kaptur Project Manager
Maximised discovery of institutions digital collections - Jisc Digital Festiv...Jisc
This workshop discussed a number of services and tools that Jisc is developing to support institutions boost the discoverability of their digital collections.
Accessibility, Inclusivity and MOOCs: What Can BS 8878 Offer?lisbk
Slides for a talk on "Accessibility, Inclusivity and MOOCs: What Can BS 8878 Offer?" given by Brian Kelly, Cetis at an ILSIG Webinar on ‘MOOCs and Inclusive Practice’ held from 12.30-13.30 on 27 March 2014.
See http://ukwebfocus.wordpress.com/events/ilsig-2014-accessibility-inclusivity-and-moocs-what-can-bs-8878-offer/
Similar to Biological Visualization Community Meetup 2014 (20)
Power to the People: Data Visualization in Biology and MedicineNils Gehlenborg
In this talk, I discuss how data visualization contributes to the democratization of data in biology and medicine. I emphasize the need to increase visualization literacy in order to achieve true democratization of biomedical data.
A Unified Approach to Exploration, Authoring, and Communication with Reproduc...Nils Gehlenborg
Visualization plays two essential roles in data-driven scientific discovery. First, visualization is a key tool for data exploration and hypothesis generation. Second, visualization facilitates communication of insights and findings. In a typical analysis scenario, however, visualization for exploration and visualization for communication are two separate processes. They often involve different software tools and data representations. Even though sophisticated interactive visualization tools are available to explore data sets, findings are usually shared in form of static images or functionally limited interactive visualizations. While these capture a particular state, they do not include any information about the exploration process that lead to the finding.
In this talk I will describe how by capturing the visual exploration process, visualizations can be made reproducible and sharable. My collaborators and I leverage such data about the analysis process to allow analysts to create "vistories", which are interactive and annotated figures, that communicate insights and findings.
Receiving the John Kendrew Award is a great honour for me, and I am humbled to be joining the ranks of the previous recipients. None of this would have been possible without the many people who influenced my career at EMBL and Harvard Medical School, in particular, my past and present mentors. To me, the John Kendrew Award is not only a recognition of my achievements. I also consider it an acknowledgment of the importance of my field—visualisation of biomedical data—which was in its infancy when I started my PhD at the EMBL-EBI in 2006.
https://www.embl.de/aboutus/alumni/news/news_2018/20180302_gehlenborg/index.html
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What is the data visualization community and what can we learn from it?
What are some great examples?
What are the reasons why we don’t see more of this work in bioinformatics? The valley death ...
Interpreting data from cohort studies where clinical and molecular data across hundreds to thousands of patient samples need to be integrated, potentially spanning multiple time points, is challenging. In this presentation, I will discuss how data visualization can be used to drive or support this process, using tools that are applying the concept of “divide and conquer” to visual exploration. I will be presenting our early work on StratomeX and illustrate how this approach led to techniques such as Domino and LineUp, and will also introduce OncoThreads and Lineage, tools that we designed for visualization of cohorts with temporal and genealogical information, respectively.
Data Visualization in Biomedical Sciences: More than Meets the EyeNils Gehlenborg
In science, data visualization serves two primary purposes. The first is to explore data sets interactively and the second is to communicate discoveries. However, the requirements for visualizations employed in these activities are very different. Therefore, the software tools used for these purposes are typically disconnected, creating significant challenges for reproducibility and effective communication of discoveries in data-driven biomedical science. In this presentation, I will address how a new approach to creating data visualization tools can connect data analysts and other stakeholders inside and outside the scientific community. I will introduce and demonstrate the "Vistories" approach that was motivated by these question.
Presented at the 5th Cancer Research UK Big Data Analytics Conference on Data Visualization.
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HiGlass + HiPiler: Making Sense of Chromosome Interaction Data with Multi-Sca...Nils Gehlenborg
How can we visualize a 3,000,000 x 3,000,000 cell matrix and allow analysts to explore features across a wide range of different scales? We built HiGlass, a web-based visualization tool for analysis of Hi-C and other genome-wide chromosome interaction data that enables comparison of multiple contact matrices and integration of other data types. To complement this functionality, we also created HiPiler, which enables investigators to view and explore thousands of features such as loops or TADs and correlate their appearance with their genomic locations and experimental conditions. In my talk, I will discuss the design of HiGlass and HiPiler and present a range of use cases for these applications.
(Thanks to Fritz Lekschas for providing many of the slides.)
Multi-Scale Visualization Tools for Exploration of Chromosome Interaction ...Nils Gehlenborg
How do you visualize a 3 million x 3 million matrix and allow users to explore features across a wide range of different scales? We built HiGlass and HiPiler, web-based visualization tools for analysis of Hi-C and other genome-wide chromosome interaction data that enables comparison of multiple contact matrices and integration of other data types. In my talk, I will discuss several use cases and describe how we architected HiGlass and HiPiler.
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The international Symposium on Biological Data Visualization (BioVis) is an interdisciplinary event covering all aspects of visualization in biology. The Symposium brings together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization as well as bioinformatics and biology researchers in state-of-the-art visualization research. In order to further engage with a biological audience, the fourth and fifth editions were organized in collaboration with the International Society for Computational Biology and held jointly with their ISMB annual conference.
We are keen to maintain a presence with the VIS community and this meetup will serve as a focus for researchers in BioVis to meet up at VIS to discuss ideas for further development of the Biological Visualisation Community. In particular, this meetup will bring together BioVis researchers and groups of interest within the City of Chicago, who runs a regular Data Visualization Meetup in Chicago. Website: http://www.meetup.com/The-Chicago-Data-Visualization-Group/
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The Refinery Platform (http://www.refinery-platform.org) is a web-based data visualization and analysis system for epigenomic and genomic data designed to support reproducible biomedical research. The analysis backend employs the Galaxy Workbench and connects to a data repository based on the ISA-Tab data description format. In my talk I will discuss the exploratory visualization tools that we have integrated into Refinery.
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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.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
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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 .
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.
1. Biological Visualization
Community Meetup
Meeting Google Doc at http://bit.ly/1u1O7dg!
Organizers
Jessie Kennedy, Edinburgh Napier University, Edinburgh, UK
Nils Gehlenborg, Harvard Medical School, Boston, USA
10 November 2014 @ IEEE VIS in Paris, France
2. Meeting Google Doc at http://bit.ly/1u1O7dg
Plan
• community activities and events
• BioVis 2014/2015/2016
• VIZBI 2015
• VCBM 2015
• BiVi Community
• ISCB COSI
• open discussion
3. Meeting Google Doc at http://bit.ly/1u1O7dg
Activities and Events
• 07/2014 - BioVis 2014 (Boston, USA)
• 11/2014 - VIS & BioVis Community Meetup (Paris, France)
• 12/2014 - BiVi 1st Annual Meeting (Edinburgh, UK)
• 03/2015 - VIZBI 2015 (Cambridge, USA)
• 07/2015 - BioVis 2015 (Dublin, Ireland)
• 09/2015 - VCBM 2015 (Chester, Uk)
• 10/2015 - VIS (Chicago, USA)
4. Meeting Google Doc at http://bit.ly/1u1O7dg
BioVis 2014 / www.biovis.net
• 11-12 July 2014 in Boston, USA
• Special Interest Group meeting at ISMB/ECCB 2015
• Keynote: Tamara Munzner (UBC)
• Challenge Speakers: Karl Broman (U Wisconsin-Madison)
& Serdar Turkarslan (Institute for Systems Biology)
• Primer Speakers: Marc Streit (JKU Linz) & Bang Wong
(Broad Institute)
• 24 other talks
5. Meeting Google Doc at http://bit.ly/1u1O7dg
BioVis 2015 / www.biovis.net
• 10-11 July 2015 in Dublin, Ireland
• Special Interest Group meeting at ISMB/ECCB 2015
• Deadlines
• Paper submission: February 15, 2015
• Poster submission: May 29, 2015
• Data Analysis Contest entry submission: May 1, 2015
• Design Contest entry submission: May 1, 2015
6. Meeting Google Doc at http://bit.ly/1u1O7dg
BioVis 2015 / www.biovis.net
• all papers will be available in IEEE Digital Library
and/or BMC Proceedings
• papers will also be considered for BMC
Bioinformatics using a 2-stage review process
7. BioVis 2015 Design
Contest
RNA Structure Evolution.
Chairs
Ryo Sakai, KU Leuven, Belgium
Eamonn Maguire, Oxford University, England
Both are here at VIS, so just speak with us for more information!
10. Meeting Google Doc at http://bit.ly/1u1O7dg
BioVis 2016 / www.biovis.net
• plan is to return to IEEE VIS
• October 2016 in Washington (DC)
• then alternate between VIS and ISMB
(1 year or 2 year cycles)
11. Meeting Google Doc at http://bit.ly/1u1O7dg
VIZBI 2015 / www.vizbi.org
• 25-27 March 2015 in Cambridge, USA
• hosted by the Broad Institute
• 20 invited speakers
• Deadlines
• poster submissions only (usually up to a week
before the event)
12. Meeting Google Doc at http://bit.ly/1u1O7dg
VCBM 2015 / www.vcbm.org
• 14-15 September 2015 in Chester, UK
• hosted by University of Chester
• Deadlines
• Paper submission: June 21, 2015
• Poster submission: August 07, 2015
13. Meeting Google Doc at http://bit.ly/1u1O7dg
International Society for
Computational Biology (ISCB)
• Website: http://www.iscb.org/iscb-cosis
• community of special interest (COSI)
• proposal for BioVis COSI will be submitted shortly
• goal is to establish a permanent presence in the
computational biology community
• organize small events (meetups, workshops, etc.) at
ISCB conferences when BioVis is taking place at IEEE
VIS
14. Meeting Google Doc at http://bit.ly/1u1O7dg
Biological Visualisation
Community / bivi.co
15. Meeting Google Doc at http://bit.ly/1u1O7dg
Biological Visualisation
Community / bivi.co
• 1st Annual Meeting
• 16-17 December 2014 in Edinburgh, UK
• hosted by Edinburgh Napier University
• Deadlines:
• submission of vis tools or data challenges via
bivi.co website
16. Meeting Google Doc at http://bit.ly/1u1O7dg
Open Discussion
• Any other announcements?
• Questions at http://bit.ly/1u1O7dg