Synthesis Infrastructures

Workshop Working Groups: Difference between revisions

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* Group Page: [[Computable Graphs]]
* Group Page: [[Computable Graphs]]
* Project Pages: [[Translate Logseq Knowledge Graph to Systems Biology Network Diagrams]]
* Project Pages:  
* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983137222467604 #logseq-systems-bio]
** [[Translate Logseq Knowledge Graph to Systems Biology Network Diagrams]]
** [[Synthesis center for cell biology]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983137222467604 #computable-graphs]


=== What ===
=== What ===
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Discussion entry points:
Discussion entry points:


[[Matthew Akamatsu]] https://discord.com/channels/1029514961782849607/1033091746139230238/1040212464631029822
* [[Matthew Akamatsu]] https://discord.com/channels/1029514961782849607/1033091746139230238/1040212464631029822


=== Who ===
=== Who ===


[[Konrad Hinsen]], based on work on leibniz-pharo and interest in computational modeling/research
* [[Akila Wijerathna-Yapa]]
 
* [[Matthew Akamatsu]] (lead?)
[[Akila Wijerathna-Yapa]]
* [[Konrad Hinsen]], based on work on leibniz-pharo and interest in computational modeling/research
 
* [[Jodi Schneider]]?
[[Matthew Akamatsu]]
 
[[Jodi Schneider]]?


=== Progress so far ===
=== Progress so far ===


https://synthesis-infrastructures.wiki/Translate_Logseq_Knowledge_Graph_to_Systems_Biology_Network_Diagrams
Some resources:


https://synthesis-infrastructures.wiki/Synthesis_center_for_cell_biology
* Simularium https://simularium.allencell.org/


Simularium https://simularium.allencell.org/
* Vivarium Collective https://vivarium-collective.github.io/
 
Vivarium Collective https://vivarium-collective.github.io/


=== Next (ideas for next steps, open problems) ===
=== Next (ideas for next steps, open problems) ===


don't know if a joint project makes sense, but perhaps coordinated first prototypes of a bridge
don't know if a joint project makes sense, but perhaps coordinated first prototypes of a bridge?


could use:
could use:


someone with programming skills to implement a POC translation between a discourse graph and one of the specific modeling languages/ontologies
* someone with programming skills to implement a POC translation between a discourse graph and one of the specific modeling languages/ontologies


== Synthesis-oriented social media aka "from the stream to the garden" ==
== Synthesis-oriented social media aka "from the stream to the garden" ==
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=== Who ===
=== Who ===


lead: [[Ronen Tamari]]
* [[Ronen Tamari]] (lead?)
 
* [[Konrad Hinsen]]
[[Konrad Hinsen]]
* [[Jonny Saunders]]
 
* this seems super relevant to [[Amy Zhang]] based on prior work on Wikum and Tilde
[[Jonny Saunders]]
* and [[Nouran Soliman]] based on LiTweeture project
 
* and [[Michael Toomim]] and team based on their work on peeryview
this seems super relevant to [[Amy Zhang]] based on prior work on Wikum and Tilde
 
and [[Nouran Soliman]] based on LiTweeture project
 
and [[Michael Toomim]] and team based on their work on peeryview


=== Progress so far ===
=== Progress so far ===
https://synthesis-infrastructures.wiki/Linked_Data_Publishing_On_Activitypub#Linked_Attention_Data_Publishing


Resources
Resources


BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/
* BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/
 
* [[Fediverse]]
[[Fediverse]]
* [[Mastodon]]
 
* [[ActivityPub]]
[[Mastodon]]
 
[[ActivityPub]]


[[bengo]] started a thread with a prototype of expressing a graph of info using both ActivityStreams and SEPIO ontologies - https://discord.com/channels/1029514961782849607/1033091723389317160/1040042059916120094
[[Benjamin Goering]] started a thread with a prototype of expressing a graph of info using both ActivityStreams and SEPIO ontologies - https://discord.com/channels/1029514961782849607/1033091723389317160/1040042059916120094


=== Next (ideas for next steps, open problems) ===
=== Next (ideas for next steps, open problems) ===
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could use:
could use:


a "user" (preferably non-technical) to give feedback on mental models here. maybe pooja?
* a "user" (preferably non-technical) to give feedback on mental models here. maybe [[Pooja Upadhyay]]?


== Extending semantic mediawiki to cover discourse graph modeling ==
== Extending semantic mediawiki to cover discourse graph modeling ==
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It could be really valuable to try to prototype a "computable" synthesis of the knowledge in this workshop here in the wiki. One test of the "computability" would be to make it visualizable.
It could be really valuable to try to prototype a "computable" synthesis of the knowledge in this workshop here in the wiki. One test of the "computability" would be to make it visualizable.


Could have applications to thesemantic climate setting that [[Peter-Murray Rust]] is working on
Could have applications to thesemantic climate setting that [[Peter Murray-Rust]] is working on


See discussion in <code>#discourse-modeling</code> channel
See discussion in <code>#discourse-modeling</code> channel
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=== Who ===
=== Who ===


[[Kyle McLaury]]
* [[Kyle MacLaury]]
 
* [[Peter Murray-Rust]]
[[Peter-Murray Rust]]
* [[Karola Kirsanow]]?
 
* [[Joel Chan]] also interested in assisting
[[Karola Kirsanow]]?
 
[[Joel Chan]] also interested in assisting


=== Progress so far ===
=== Progress so far ===
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* [[Discourse Modeling]]
* [[Discourse Modeling]]
* [[Making Discourse Graphs Indexable & Discoverable]]
* [[Making Discourse Graphs Indexable & Discoverable]]
Resources


=== Next (ideas for next steps, open problems) ===
=== Next (ideas for next steps, open problems) ===
A bit unformed at the moment.
Might be best to start off by just talking!


= Latent/forming =
= Latent/forming =
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=== What ===
=== What ===


how do we define minimal information models tuned for synthesis that can interoperate across various disciplines?
How do we define minimal information models tuned for synthesis that can interoperate across various disciplines?
 
concrete problem expressed by [[Peter-Murray Rust]] here: https://discord.com/channels/1029514961782849607/1040214388554084372/1040299259930611833: "The idea of Hypothesis testing is common in some disciplines, unknown in others. For example chemical synthesis or materials science is "can we make X?" and many sciences are exploratory - what can we see with a new telescope, plants in Antarctica, etc. You have to design your project but I suspect Hypothesis doesn't come into it."


and to a certain extent, the issue of representing/discussing the discourse of computational research (e.g., model parameters), discussed by [[Konrad Hinsen]] here: https://discord.com/channels/1029514961782849607/1038988750677606432/1039576903838859326


this connects with [[Peter-Murray Rust]]'s work on semantic climate (semantifying the IPCC report)
Concrete problem expressed by [[Peter-Murray Rust]] here: https://discord.com/channels/1029514961782849607/1040214388554084372/1040299259930611833: "The idea of Hypothesis testing is common in some disciplines, unknown in others. For example chemical synthesis or materials science is "can we make X?" and many sciences are exploratory - what can we see with a new telescope, plants in Antarctica, etc. You have to design your project but I suspect Hypothesis doesn't come into it."


see discussion here: https://discord.com/channels/1029514961782849607/1040057721044598788/1040060670907002973


and here: https://discord.com/channels/1029514961782849607/1033091746139230238/1040226423346040853
And to a certain extent, the issue of representing/discussing the discourse of computational research (e.g., model parameters), discussed by [[Konrad Hinsen]] here: https://discord.com/channels/1029514961782849607/1038988750677606432/1039576903838859326


but also to emerging discussions around interoperability and Surfacing/managing/resolving disagreements in ontologies/terms/federation


=== Who ===
This connects also with [[Peter-Murray Rust]]'s work on semantic climate (semantifying the IPCC report).


[[Joel Chan]] is definitely interested in this, happy to lead this
* see discussion here: https://discord.com/channels/1029514961782849607/1040057721044598788/1040060670907002973
* and here: https://discord.com/channels/1029514961782849607/1033091746139230238/1040226423346040853


[[Peter-Murray Rust]]
And also connects to emerging discussions around interoperability and Surfacing/managing/resolving disagreements in ontologies/terms/federation


Possibly also [[James Howison]], based on emphasis in workshop submission on software artifacts as a locus of synthesis
=== Who ===


And [[Paul Itoi]] based on interest in multiplayer zettelkastens
* [[Joel Chan]] is definitely interested in this, happy to lead this
* [[Peter Murray-Rust]]?
* Possibly also [[James Howison]], based on emphasis in workshop submission on software artifacts as a locus of synthesis
* And [[Paul Itoi]] based on interest in multiplayer zettelkastens


=== Progress so far ===
=== Progress so far ===
Resources


=== Next (ideas for next steps, open problems) ===
=== Next (ideas for next steps, open problems) ===
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=== Who ===
=== Who ===


[[Jordan Wick]], based on work on "explain paper like i'm 5": https://github.com/epli-org/epli
* [[Elianna DeSota]]: https://discord.com/channels/1029514961782849607/1033091572167888926/1036629378567770223 - "I would love to explore how we might better navigate the increasing 'bits' of knowledge and research that we are publishing and sharing among our communities, and new + better ways of thinking about how to synthesize and evaluate the relationships between different fields of research."
* [[Joseph Chee Chang]]: https://discord.com/channels/1029514961782849607/1033091572167888926/1040001880002154546
* [[Jordan Wick]], based on work on "explain paper like i'm 5": https://github.com/epli-org/epli


=== Progress so far ===
=== Progress so far ===
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=== Who ===
=== Who ===


possibly interested:
* [[Matt Clancy]]: https://discord.com/channels/1029514961782849607/1033091746139230238/1037560902800658514
 
* [[Eirini Malliaraki]]
[[Eirini Maliaraki]]
 
[[Pao Siangliulue]], based on past work on integrated crowdsourcing
 
Maybe also and [[Nouran Soliman]] based on LiTweeture project
 
And [[Angelina Lesnikova]] and [[Valerii Kremnev]] based on the sci2sci approach of integrating publishing into lab notebooks


[[Jay Patel]], based on expressed interests in reimagining peer review processes
* [[Martin Karlsson]]: https://discord.com/channels/1029514961782849607/1033091746139230238/1039238852721770556
* [[Karola Kirsanow]]: https://discord.com/channels/1029514961782849607/1033091746139230238/1039228139366268938
* [[Matthew Evans]]: https://discord.com/channels/1029514961782849607/1033091597635694694/1036658723596279868


[[Wayne Lutters]]?
* [[Pao Siangliulue]], based on past work on integrated crowdsourcing
* Maybe also and [[Nouran Soliman]] based on LiTweeture project
* And [[Angelina Lesnikova]] and [[Valerii Kremnev]] based on the sci2sci approach of integrating publishing into lab notebooks
* [[Jay Patel]], based on expressed interests in reimagining peer review processes
* [[Wayne Lutters]]?


=== Progress so far ===
=== Progress so far ===
Resources


=== Next (ideas for next steps, open problems) ===
=== Next (ideas for next steps, open problems) ===
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=== Who ===
=== Who ===


[[Konrad Hinsen]] and [[Jonny Saunders]]: https://discord.com/channels/1029514961782849607/1038988750677606432/1040172075773607956
* [[Konrad Hinsen]] and [[Jonny Saunders]]: https://discord.com/channels/1029514961782849607/1038988750677606432/1040172075773607956


=== Progress so far ===
=== Progress so far ===
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== Hidden value / mental model mismatches in transitions between workflows / tools ==
== Hidden value / mental model mismatches in transitions between workflows / tools ==
* Group page: [[Mental Models]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1040470706271555706 #mental-models]


=== What ===
=== What ===


What hidden value / mental mismatches might there be between new infrastructures we want to build (e.g., ontology-based organization of knowledge) and existing workflows / tools amongst scientists?
What hidden value / mental (mis)matches might there be between new infrastructures we want to build (e.g., ontology-based organization of knowledge) and existing workflows / tools amongst scientists?


=== Who ===
=== Who ===


[[Pooja Upadhyay]]: https://discord.com/channels/1029514961782849607/1038594946791387276/1039242312615735346
[[Pooja Upadhyay]]: https://discord.com/channels/1029514961782849607/1038594946791387276/1039242312615735346
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twitter (centralized platform) to mastodon (decentralization, federation)
twitter (centralized platform) to mastodon (decentralization, federation)


[[Peter-Murray Rust]]
[[Peter Murray-Rust]]


e.g., ontologies vs. dictionaries
e.g., ontologies vs. dictionaries
Joelchan
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