Saturday, May 4, 2019

Common fruit fly: Stanford Ph.D. Chris Q. Doe - Stanford Bio-X Frontiers in Interdisciplinary Biosciences Seminar, "Development and function of locomotor circuits in Drosophila," ... What is TensorFlow? * * * Stanford Wikidata Affinity Group - Hilary Thorsen - "Since the future calls will be topic-based, can you tell me more about what work you are doing with Wikidata?," Scott - I do University work with Wikidata, in terms of thinking and envisioning (e.g. planning, design, and conceptualizing) World University and School in Wikidata



Dear Chris (and Julia), 

Thanks for your excellent and far-reaching talk at Stanford on Thursday: "Chris Doe - Stanford Bio-X Frontiers in Interdisciplinary Biosciences Seminar, "Development and function of locomotor circuits in Drosophila"." Thanks too for your fascinating Drosophila research and experiments re mechanisms generating neuronal diversity in the mammalian CNS - 

"We are interested in how neuronal diversity is generated, how it is used to establish neuronal circuits, and how circuits generate diverse locomotor behaviors. I will present on one of the following two topics.  In the first project, we have identified larval brain stem cells (neuroblasts) that generate the intrinsic columnar neurons of the central complex (CX), an evolutionarily conserved brain region required for celestial navigation. We have mapped the developmental origin of four columnar neuron subtypes, with the goal of (a) testing developmental mechanisms for a role in circuit assembly, and (b) testing the role of each subclass in adult navigation behaviors. In the second project, we have mapped the developmental origin of all 300 neurons in a single segment of the embryonic CNS, mapped their connectivity using ssTEM reconstruction, and are using this information to correlate developmental mechanism with connectivity. We have identified circuit features that map to clonally-related neurons (common neuroblast) or to temporally-related neurons (common birth-order), and are currently testing each mechanism for a role in motor circuit assembly and function"
https://events.stanford.edu/events/808/80887/. It was very nice to meet you both as well. The questions I'm asking have to do with how best to model digitally your research and experiments, and even in new ways, both dynamically, and as part of the whole organism, for two. 

Here's Tom Dean's Stanford Neuroscience talk from October of 2016 which I asked if I could send you:
4. Automatically Inferring Meso-scale Models of Neural Computation


Tom connects the molecular with the behavioral neural computationally (not neural circuitry-wise) using Google infrastructure in modeling part of a Drosophila fly brain (which could well have many implications for modeling mice brains as well, Julia). 

Am curious how your experimentalism and modeling, Chris, could engage Tom Dean's brain research computationally (and especially re Google infrastructure). 

What is the name again please of the brain annotation software that you use? I couldn't find 'CatMade' brain software when I searched. 

At the podium after your talk, and in asking you about Wikidata / Wikibase (Wikipedia's structured knowledge database in ~300 languages), am curious too about developing Wikidata libraries for both molecular and cellular, and 'street view' levels for brain research, as well (see, too re the MIT OCW here - https://wiki.worlduniversityandschool.org/wiki/Brain_and_Cognitive_Sciences - for example, where related courses for degrees are planned in all ~200 countries' main languages, and with a focus on brain science and language virtually/digitally, for online degrees). Wikidata seems like potentially or possibly a great resource for the CatMade brain annotating processes you mentioned a number of times. It's building on the existing brain modeling digital programs, such as CatMade, and infrastructure that World University and School also seeks to facilitate - and in creating a realistic virtual earth for brain science (am thinking here Google Street View with TIME SLIDER / Maps / Earth / TensorFlow, Translate, and esp. Poly +, ... and with avatar bots of Drosophila and Mice organisms, with brains, and even evolutionary biology ecosystems over time). How best could or might we build on your tremendous knowledge, Chris, and add and develop your research in new ways into a Tom Dean-informed Stanford/Google-centric platform, I wonder? 

Julia, I noticed that your research is focusing on "Understanding neuronal circuitry underlying locomotion, sexual function and motility" - 
http://med.stanford.edu/kaltschmidt-lab.html . Fascinating and timely, and central to the evolution of all sexual species out of the estimated 3- 100 million species (8.7 million?) and since life began! 

I'm very interested in studying related questions, but from very different but interweaving perspectives, in my actual-virtual, physical-digital Harbin Hot Springs' ethnographic field research, and especially in creating a realistic virtual Harbin for STEM research (am thinking Google Streetview with Time Slider at the cellular and atomic levels too, and for brain science). So, for example, and brainstorming-wise, in people (e.g. 'human primates'?) soaking in the Harbin Hot Springs' warm pool, and in studying in a related vein, questions of enjoyments, and even loving bliss neurochemistry elicitation, how could one also add rigorous in situ STEM research into the "neuronal circuitry underlying locomotion, sexual function and motility" in humans, I wonder? Could one put on (HUMM, which I learned of at Stanford) head bands on people with sensors in them that are beginning to examine brain function, and stream this data back via wireless internet into a realistic virtual earth with individuals and species in it, and even with emergent models of, and data about, their brains, I wonder? 

Here's what I have in mind by a 3D interactive realistic virtual universe / earth and am planning too for the atomic / cellular levels in something like Google Street View with TIME SLIDER / Maps / Earth / Translate +++ : Visit the Harbin Hot Springs' gate here, and "walk" "4 miles" down the road to "amble" around Middletown, CA: http://tinyurl.com/p62rpcg ~ https://twitter.com/HarbinBook ~ http://bit.ly/HarbinBook ~ While Street View and the Google platform have a ways to go, I think it's the best (launching) platform for a variety of reasons. But great numbers of brain researchers will be needed for this as well. (Perhaps CC-4 MIT OCW-centric wiki World University and School's matriculated students in ~200 countries' official / main languages can help with this with time). How to begin? 

And how best to combine Tom Dean's computational neural artificial intelligence research with both of yours, Chris and Julia, and grow digital modeling and research of brain circuitry at a variety of levels, and in a myriad of ways, are further questions I have? Thank you again for your great and superb experiments and talk at Stanford on Thursday - "Development and function of locomotor circuits in Drosophila" - and looking forward to communicating about all of this further with time as well. Thank you so much. 

All the Best, Scott
- http://scottmacleod.com/papers.htm
- CV: https://goo.gl/JZheSb

Scott MacLeod - https://twitter.com/scottmacleod   

World Univ and Sch Twitter - http://twitter.com/WorldUnivandSch

Languages - World Univ - http://twitter.com/sgkmacleod   


“Naked Harbin Ethnography” book (in Academic Press at WUaS) - http://twitter.com/HarbinBook

(OpenBand (Berkeley) - https://twitter.com/TheOpenBand ) )
















-- 
- Scott MacLeod - Founder, President & Professor

- World University and School

- 415 480 4577

- CC World University and School - like CC Wikipedia with best STEM-centric CC OpenCourseWare - incorporated as a nonprofit university and school in California, and is a U.S. 501 (c) (3) tax-exempt educational organization. 



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2 preprints our today from Chris Q. Doe lab with rich, newly mapped neural circuitry of larval #Drosophila:

Premotor circuits for segment A1 + muscle activity imaging https://www.biorxiv.org/content/10.1101/617977v1 …

Genetics of neural diversity and connectivity: https://www.biorxiv.org/content/10.1101/617936v1 …

with @ZarinAref


https://twitter.com/albertcardona/status/1121595737685528577


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Congrats to GSA members elected to @AmericanAcad of Arts&Sciences: Nancy Bonini, Chris Q. Doe, and Sabeeha Merchant http://bit.ly/1gV7ies


https://twitter.com/GeneticsGSA/status/459441203617210369


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Today at 4PM @StanfordBioX "Frontiers in Interdisciplinary Biosciences" Pre-Seminar presentation by Dr. Julia Kaltschmidt:


https://twitter.com/TopNeuroDocs/status/1123277073789935617


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An interview with our founder Dr @tim_fiori featured today in Medgadget - check it out to learn more about the science behind Edge!


https://twitter.com/HummTech/status/1072587950372855809


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Early takeaway from the 2019 BrainMind conference at @MIT paraphrased from @M_McCullough_MD : “we’re on the verge of a watershed moment for brain science, akin to unlocking the power of the atom”


https://twitter.com/HummTech/status/1124676203485335553


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HUMM is building a safe and cost effective way to bring this incredible technology out of lab and into everyday life.  We're launching next month, subscribe to updates at http://www.humm.tech

Like they say - don't try this at home - try HUMM instead!


https://twitter.com/HummTech/status/1118045998712885248


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What is TensorFlow?
Siraj Raval: @TensorFlow in 5 Minutes (tutorial)
https://youtu.be/2FmcHiLCwTU  > Machine_Learning
-https://wiki.worlduniversityandschool.org/wiki/Machine_Learning …
-https://wiki.worlduniversityandschool.org/wiki/Artificial_Intelligence …
-https://wiki.worlduniversityandschool.org/wiki/Computer_Science … Check out the best STEM CC-4 MIT OpenCourseware for free degrees for #RealisticVirtualEarth?


https://twitter.com/WorldUnivAndSch/status/1124741666127040512


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What is TensorFlow? | Introduction to TensorFlow | TensorFlow Tutorial for Beginners | Simplilearn https://youtu.be/E8n_k6HNAgs > Machine_Learning https://wiki.worlduniversityandschool.org/wiki/Machine_Learning … -https://wiki.worlduniversityandschool.org/wiki/Artificial_Intelligence … -https://wiki.worlduniversityandschool.org/wiki/Computer_Science … Check out the best STEM CC-4 MIT OpenCourseware for free degrees


https://twitter.com/WorldUnivAndSch/status/1124738530888994817




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Scott MacLeod
Fri, May 3, 7:21 AM (1 day ago)
to Lydia, Hilary

Hi Hilary,

Thanks again for this great opportunity. As an editable agenda, I thought to add World University and School (planned as major Wikidata-informed university libraries and in ~200 countries' main / official languages, and in all ~7,111 known living languages +) - Agenda: https://docs.google.com/document/d/1jxb01FcixSFx8mOUyTpRHbbjsm2bgB4fTQt9jjpKOR0/edit?usp=sharing - but I wanted to ask you first. Would it be alright to add WUaS to this Wikidata Affinity Group list of cohort Universities? WUaS seeks to become the Harvard of the internet as major and excellent research universities in each of all ~200 countries' languages. Thank you.

Cheers, Scott

World Univ and Sch Twitter - http://twitter.com/WorldUnivandSch

Languages - World Univ - http://twitter.com/sgkmacleod

WUaS Press - https://twitter.com/WUaSPress

--

--
- Scott MacLeod - Founder & President
- World University and School
- http://worlduniversityandschool.org

- 415 480 4577
- http://scottmacleod.com


- CC World University and School - like CC Wikipedia with best STEM-centric CC OpenCourseWare - incorporated as a nonprofit university and school in California, and is a U.S. 501 (c) (3) tax-exempt educational organization.



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Hilary K Thorsen
Fri, May 3, 2:55 PM (21 hours ago)
to me

Hi Scott,


The cohort institutions that will be sharing at the meeting on May 7th are part of the Linked Data for Production grant. We didn't have time to talk about their projects at the first meeting. Since our agenda for this next meeting already should cover the full hour, I don't want to add anything new.

Since the future calls will be topic-based, can you tell me more about what work you are doing with Wikidata?


Thanks,

Hilary




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Hi Hilary, (and Lydia, who's WUaS's contact person),

thanks for your email, and this information. Congratulations too to all of these cohort institutions on your Linked Data for Production grant! I do University work with Wikidata, in terms of thinking and envisioning (e.g. planning, design, and conceptualizing) World University and School in Wikidata. 

As I wrote in the Wikidata Affinity Group 4/23/19 Meeting Notes: 

WUaS is developing "university libraries for matriculating students (Bachelor, Ph.D., M.D. Law, and I.B.) in each of ~200 countries’ official / main languages; WUaS donated itself for co-development to Wikidata in its ~300 languages in 2015 and got WUaS Miraheze MediaWiki in 2017, but they’re not yet inter-operable re libraries and Linked Open Data." In a sense WUaS donated ~200 major online universities, 7,1111 wiki schools in each of all living languages, music schools in same, as well as plans for online libraries and online museums (in a realistic virtual earth), plus more ... all to emerge from Wikidata as structured knowledge database. WUaS also donated plans for an universal translator in all known living languages for co-development to Wikidata as well.  

Having said that, WUaS has been seeking to work on Wikidata in new ways as "back end" with our "front end" WUaS Miraheze MediaWiki, but they haven't been joined yet (since 2017). Connecting them through an HTML-editable Miraheze MediaWiki which is in the works will open multiple directions for working with Wikidata. (And potentially our WUaS matriculating online students in each of all ~200 countries' main / official languages, too, will be able to help with working on Wikidata). 

Will share with you too an upcoming blog post to Stanford neuroscientists Julia Kaltschmidt and Chris Doe (who just spoke on Thursday - https://events.stanford.edu/events/808/80887/) about Wikidata libraries re molecular and cellular levels for brain research, as well (see, too the MIT OCW here - https://wiki.worlduniversityandschool.org/wiki/Brain_and_Cognitive_Sciences - for example, where related courses for degrees are planned in all ~200 countries' main languages, and with a focus on brain science and language virtually/digitally). 

Thanks very much for the Wikidata Affinity Group, and looking forward to Tuesday, May 7th's. 

Cheers, Scott 
Much of this Wikidata university work is here in these 2 'Wikipedia' and 'Wiki' blog labels:



Tuesday, May 7th at 9am PST / 12noon EST / 5pm GMT / 6pm CET. 





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Common fruit fly: Chris Doe-Stanford Bio-X Frontiers in Interdisciplinary Biosciences Seminar "Development and function of locomotor circuits in Drosophila," What is TensorFlow? Wikidata Affinity Group - I do University work with Wikidata, re envisioning https://scott-macleod.blogspot.com/2019/05/common-fruit-fly-stanford-chris-doe.html ~


https://twitter.com/WorldUnivAndSch/status/1124825349915680769


* * *
May 5, 2019

Hi, Hilary and Lydia, 

Perhaps Stanford Neuroscientist Julia Kaltschmidt (correct spelling) will be interested in exploring developing atomic and cellular level Wikidata libraries for modeling and mapping species' brains ... (I just met Julia at Chris Q. Doe's talk at Stanford on Thursday ... https://scott-macleod.blogspot.com/2019/05/common-fruit-fly-stanford-chris-doe.html).

In terms of the University work I do with Wikidata continued, there are about 725 World Univ & Sch Miraheze MediaWiki wiki pages, e.g. https://wiki.worlduniversityandschool.org/wiki/Subjects, and all of these wiki/Wikidata 'Subject' pages at WUaS, and in each of all 7,111 living languages, will connect with online libraries, e.g. here https://wiki.worlduniversityandschool.org/wiki/Library_Resources, planned in all of these languages too.

See you in the Wikidata Affinity Group on Tuesday!

Cheers, Scott



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Sunday, May 5, 2019

 Hi Scott,

I got your email (maybe Julia’s email was incorrect) and I appreciate your comments at my talk and in the email.

Quicklly, the CATMAID initial paper is here 
and here

I’ll respond to the rest of your email after I have thought it over a bit more, and checked out the Tom Dean video. 

Best wishes
Chris


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Hi Chris, and Julia, 

Thanks so much for your email, Chris, this evening, (and I had found Julia's correct email when I re-sent - thanks), and especially for the information about CATMAID software+. I've blogged about your talk a little here - http://scott-macleod.blogspot.com/2019/05/common-fruit-fly-stanford-chris-doe.html?m=0 - (and added more information about many things, but also about HUMM potentially for human brain research - https://twitter.com/HummTech/status/1124676203485335553). I've also added information to this blog post about Stanford's Wikidata Affinity Group, and re its Stanford librarian and newly Stanford Wikidatan/Wikimedian in Residence, HIlary Thorsen, who might be interested in the brain data libraries, and is potentially very helpful. Wikidata is Wikipedia's "back end" structured knowledge database in Wikipedia's 300+ languages, and is based out of Berlin. I know its head project manager Lydia Pintscher, as well as its co-founders, Denny Vrandecic (now at Google in SF Bay Area), and Markus Kroetzsch (all of whom studied at Karlsruhe / received their Ph.D.s there), and who are also potentially very helpful. And I'll e-mail introduce you to HIlary and Lydia, if the opportunity emerges. 
Thanks again, Chris. 

With all best wishes, Scott 





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