Thursday, January 30, 2025

Strix occidentalis caurina (northern spotted owl): Dear European Molecular Biology Laboratory EMBL-EBI, Aleena (Mushtaq Stolworthy), Anna (Swan), Ewan (Birney, EMBL Director), MIT Media Lab HTGAA faculty lead David (Sun Kong), Harvard and MIT Professor of Genetics' George (Church), Peter (Norvig, Google AI Director), All, Greetings, and thanks for the great Ensembl Genome Browser (2025) presentation yesterday Th 1/29/25 from near Cambridge England - Introducing the new Ensembl Genome Browser (2025) https://youtu.be/K7cmwK1ODnc . Asked - Where might the time function of a changing genome over the life of an organism become part of the ENSEMBL browser? (At MIT OCW-centric wiki World Univ & Sch we are seeking to create a #RealisticVirtualEarthForGenomics (in 1 iterating #RealisticVirtualEarth and see Peter Norvig's INCREDIBLE #ToolifyAIWUaS article ... * And how to bring together, potentially, the developing EMBL Ensembl Genome Browser with the 2025 edition of ‘How To Grow (Almost) Anything’ (HTGAA) synthetic biology course (from MIT and Harvard for registered students, as well as #GlobalListeners like myself) ?

 


https://worlduniversityandschool.blogspot.com/2025/01/strix-occidentalis-caurina-northern.html

https://scott-macleod.blogspot.com/2025/01/strix-occidentalis-caurina-northern.html



* 

Dear European Molecular Biology Laboratory EMBL-EBI, Aleena (Mushtaq Stolworthy), Anna (Swan), Ewan (Birney, EMBL Director), MIT Media Lab HTGAA faculty lead David (Sun Kong), Harvard and MIT Professor of Genetics' George (Church), Peter (Norvig, Google AI Director), All, 

Greetings, and thanks for the great Ensembl Genome Browser (2025) presentation yesterday Th 1/29/25 from near Cambridge England - 

Introducing the new Ensembl Genome Browser (2025)
https://youtu.be/K7cmwK1ODnc .

Asked - 

Where might the time function of a changing genome over the life of an organism become part of the ENSEMBL browser? (At MIT OCW-centric wiki World Univ & Sch we are seeking to create a #RealisticVirtualEarthForGenomics (in 1 iterating #RealisticVirtualEarth and see Peter Norvig's INCREDIBLE #ToolifyAIWUaS article mentioning a realistic virtual earth for the first time other than WUaS's facilitating this - https://www.toolify.ai/ai-news/revolutionizing-education-with-machine-learning-and-ai-2574306 - "Revolutionizing Education with Machine Learning and AI: #WorldUniversityInSchool ) - thinking Google Street View with time slider, #GCellView, #GMoleculeView, #GMaps with #TensorFlowAI and potentially with Pegman in G Street View becoming #AvatarAgentElectronicHealthRecords not only for humans but for many species, and individuals  - with a focus on coding for the time aspect of genome changes, and regarding the phenotype, and even for aging reversal genomics' emerging gene drug therapies in a #RealisticVirtualEarthForPharma … Asked and found “AI Overview
Yes, the genomes of species change with age. These changes include DNA methylation, mutations, and changes in gene expression”)



And how to bring together, potentially, the developing EMBL Ensembl Genome Browser with the 2025 edition of ‘How To Grow (Almost) Anything’ (HTGAA) synthetic biology course (from MIT and Harvard for registered students, as well as #GlobalListeners like myself), beginning Tu 2/4/25?

And in doing so, how to create a #RealisticVirtualEarthForGenomics, a #RealisticVirtualEarthForAgingReversal and even an #AgingReversalMachine (eg in a Physical-Digital #WUaSHospitalRoom eg view #GStreetViewRoom -https://youtu.be/q9FBhEAXRY4 ... and with EMBL at the molecular level)?

Scott









PS


https://www.linkedin.com/in/anna-swan-9732893a/?originalSubdomain=uk


slides





PPS
my notes



Aleena Mushtaq Stolworthy





PPPS

HTGAA 2025 BioBootCamp Google Document (for the just past MWF)- 

https://docs.google.com/document/d/1YhwSAjz6cwbYmRG7y1h-YYZSjI_454Sk-KV6XmEUrdk/edit?usp=sharing (with links to 3 ~3 hour-long BioBootCamp video)



PPPSa 

Part I (Monday, January 20, 9 AM – 12 PM ET)

Summary: This session introduces core biology concepts, from the central dogma to emerging applications such as phage therapy and genetic circuits. Participants will gain a solid foundation in DNA/RNA structure and function, genome engineering, and circuit design.

Part I Topics & Agenda

  • Bio Basics

    • Speaker: Anna-Thérèse Mehra

    • Subtopics: Tree of life, DNA/RNA/proteins, central dogma

  • DNA Design & Genome Engineering Methods

    • Speakers: Dominika Wawrzyniak and Michelle Yue

    • Subtopics: DNA/gene structure, mutations, vectors, CRISPR, and other DNA modifiers

  • Phage Therapeutics

    • Speaker: Lisa Riedmayr 

    • Subtopics: Introduction to bacteriophages, the need for phage therapy, future directions

  • Genetic Circuits

    • Speakers: Johannes Stein

    • Subtopics: Basic components of genetic circuits, elements required, applications

Presentation Slides: Part I and Recording: Link


PPPSb

Part II (Wednesday, January 22, 9 AM – 12 PM ET)

Summary: The second session focuses on the scientific method, experiment design, and essential laboratory techniques. Participants will learn about literature research, molecular biology tools, and best practices for conducting and documenting experiments.

Part II Topics & Agenda

  • Scientific Method & Experimental Design (30 min)

    • Speaker: Rana Said

    • Subtopics: Defining a problem, designing experiments, establishing controls, laboratory notebooks

  • Literature Research (15 min)

    • Speaker: Dominika Wawrzyniak 

    • Subtopics: Effective literature searching, PubMed, Google Scholar

  • Tools for Molecular Biology (30 min)

    • Speakers: Adrian Filips & Rana Said

    • Subtopics: Online databases, DNA synthesis, metabolic engineering tools

  • Wet Lab Methods (90 min)

    • Speakers: Jieming Chu, Adrian Filips, Martina Armas, Benjamin Arias

    • Subtopics:

      • Biosafety and sterile techniques

      • Culturing microorganisms 

      • DNA extraction and sequence analysis

      • DNA cloning/assembly: PCR, restriction-ligation, Gibson assembly, gel electrophoresis, cell transformation

  • Scientific Figures (15 min)

    • Speaker: Dominika Wawrzyniak

    • Subtopics: Creating clear and accurate scientific images

Presentation Slides: Part II and Recording: Link




PPPSc

Part III (Friday, January 24, 9 AM – 12 PM ET)

Summary: The third session dives into coding and software tools for bioinformatics. Participants will practice Python fundamentals, explore Google Colab for biological data analysis, and learn how to perform in silico cloning using Benchling.

Part III Topics & Agenda

  • Python Fundamentals & Colab (60 min)

    • Speaker: Paul Kao

    • Subtopics: Fundamentals of Python, Basic Syntax, Setting up Colab

  • Colab Examples and AI Tools (45 min)

    • Speaker: Suvin Sundararajan

    • Subtopics: From Code to Lab: Practical Applications with CoLab & Opentrons

  • Benchling Basics (60 min)

    • Speaker: Cholpisit (Ice) Kiattisewee

    • Subtopics: Reading DNA sequences, in silico cloning by scenario, essential Benchling features

  • Accessible Biolabs (15 min)

    • Speaker: Adrian Filips

    • Subtopics: Setting up labs with limited resources, accessible protocols for external students

Presentation Slides: Part III and Recording: Link



PPPPPS

David Sun Kong, Ph.D.
@davidsunkong
·
Jan 7
I’m thrilled to announce that the application for the 2025 edition of our
@medialab
 and global synthetic biology course, “How to Grow (Almost) Anything” is now open! Application link in thread 👇

https://x.com/davidsunkong/status/1876687155604631779



PPPPPS
A Related set of Tweets 

Apply to be a #GlobalListener or student in this #MITHarvard course @GihanJaya ? How best to grow a #WetLab & #VirtualDrosophila in 1 #RealisticVirtualEarth & in a #RealisticVirtualEarthForGenetics (& esp in #RealisticVirtualHarbin @HarbinBook eg for #EthnoWikiVirtualWorldGraphy)?

https://x.com/WorldUnivAndSch/status/1877848832978944013

https://x.com/scottmacleod/status/1877849225419006195

https://x.com/Q_YogaMacFlower/status/1877849090182042080

https://x.com/sgkmacleod/status/1877850123096490177

https://x.com/HarbinBook/status/1877849954955194399

https://x.com/WUaSPress/status/1877849850907107607

https://x.com/TheOpenBand/status/1877904718854574529




Retweeting -

David Sun Kong, Ph.D.
@davidsunkong
·
Jan 7
I’m thrilled to announce that the application for the 2025 edition of our
@medialab
 and global synthetic biology course, “How to Grow (Almost) Anything” is now open! Application link in thread 👇

https://x.com/davidsunkong/status/1876687155604631779



PPPPPPS

A further related set of Tweets re aging reversal and extreme longevity genetic drug therapies in a #RealisticVirtualEarth - 

An #AgingReversalMachine as #WUaSMultimediaHospitalRoom re view #GStreetViewRoom -https://youtu.be/q9FBhEAXRY4 & #eRapid -https://wyss.harvard.edu/technology/erapid-multiplexed-electrochemical-sensors-for-fast-accurate-portable-diagnostics/ for all ~200 countries' hospitals & online #WUaSAcademicMedicalCenter in online #WUaSHospitals too & w @geochurch https://youtu.be/bnCEIPQFNnk ~








PPPPPPPS

In what ways could ByronHannMD build an #NDimensional #WUaSHospitalRoom in #Canyon94516

In what ways could #ReedCollege friend #ByronHannMD "float" or "fly" a #PrincetonUniv #FlywireConnectome #DrosophilaFlyBrain in middle of #WUaSMultimediaRoom ...?


In what ways could #ReedCollege friend #ByronHannMD "float" or "fly" a #PrincetonUniv #FlywireConnectome #DrosophilaFlyBrain in middle of #WUaSMultimediaRoom https://youtu.be/q9FBhEAXRY4 after building a #NDimensional #WUaSHospitalRoom in #Canyon94516 and at the molecular level -for aging reversal


. . . 

?#ByronHannMD Build #NDimensional #WUaSHospitalRoom in #Canyon94516 #CitizenScience #FlywireConnectome as #AgingReversalMachine w #GMoleculeLevel
https://youtu.be/q9FBhEAXRY4 w #AvatarAgentElectronicHealthRecords w @geochurch https://m.youtube.com/watch?v=bnCEIPQFNnk?










PPPPP PPPPS

Introducing the new Ensembl Genome Browser (2025)
https://youtu.be/K7cmwK1ODnc

Slides -

Questions - 

(from 2024 - 
Studying genes and genomes with Ensembl genome browser (2024)



* 

Thank you for attending Introducing the new Ensembl Genome Browser


Hi Scott GK MacLeod,
Thank you for attending Introducing the new Ensembl Genome Browser. We hope you enjoyed the event.

Please submit your questions or comments to: webinars@ebi.ac.uk.
The recording of this webinar is now available here on the EMBL-EBI Training site: https://www.ebi.ac.uk/training/events/introducing-new-ensembl-genome-browser/

And on YouTube: https://www.youtube.com/watch?v=K7cmwK1ODnc

The slides are also available: https://docs.google.com/presentation/d/1zk3a9D1PtsnKRbyybO3kJtDZ91NSEjJqQyCd9pFS-MI/edit#slide=id.g32a43ec4c5e_0_1619

There were many questions asked during the webinar, they are detailed here: https://docs.google.com/spreadsheets/d/12SgsS7s4lPpZmYk2GQmi25fLuFaGfTdEFEC1NNE2Kkg/edit?usp=sharing

We also have lots more on-demand training that’s openly available to access anytime: https://www.ebi.ac.uk/training/on-demand

Happy learning!

Anna

Dr Anna Swan
Senior Scientific Training Officer - Digital Learning
Pronouns: her/she
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
www.ebi.ac.uk/training | @EBItraining
Thank you!



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https://en.wikipedia.org/wiki/Northern_spotted_owl

https://commons.wikimedia.org/wiki/Category:Strix_occidentalis

https://species.wikimedia.org/wiki/Strix_occidentalis_caurina


heard this owl I think in the middle of the night from the HI SF Fisherman's Wharf youth hostel on the north shore of SF

...



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