TBinSL:Thinking Big about the Very Small

Graham Mills

http://tidalblog.blogspot.com/http://bit.ly/listfaq

Visualization: molecules, gene data, cells...

Max Chatnoir demonstrates her giant cellon Elucian Isles

Context: TB (tuberculosis)

Downsides Bacterial infection Kills 4500 people daily Antibiotic-resistant strains Vaccines of limited use Rapidly lethal in HIV/AIDS Hard to do labwork

Upsides• Major research initiatives

aimed at developing new drugs and vaccines and eliminating TB by 2020

Molecules

Small molecules (metabolites, drugs)• Hiro Sheridan: molecule rezzer (ACS), Orac [1]

o Incorporated into metabolic browser Large molecules: proteins, etc• Prim-intensive: Troy McLuhan [2]

o Added interactivity• Sculpted: Hiro Sheridan [3]

o Added interactivity• Also: animated [4] and static textures [5], particles

• SL Molecular Structures Group (Asorel Todriya)• Lang & Bradley (2009)

http://journal.chemistrycentral.com/content/3/1/14 

Molecules in Second Life

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5

Metabolic browser

Molecules by Hiro Sheridan’s Orac and stored inTroy McLuhan’s holoemitter

Prim-intensive protein models (backbone only)

M. tuberculosiscellulase

Student work on A2M in the E. coli cell wall (2008)

A2M

Sculpted protein (+ particle)

Student group work (2009)

Students work on different genesGroups work on different speciesLink by teleport to giant TB genome

Datascape: Giant TB genome

Genes encode proteins>4000 TB genes, alltouch-sensitive

Individual genes and their products

Associations withother proteins (STRING)Contextual sub-mapSLV 2.0 texture on marker

Take your analytical tools with you: shared media dashboard

Follower is a mashup ofPuppeteer and Scratch4SL

Cellscape: porins, alveolus, macrophage

Cityscape: The Cure

Robert Koch’s lab

TB timeline maze (under construction)

TB started hereAnd is a major problem here

Conclusions

Progress has been made so let’s share it!

It’s not content, it’s collaboration Reasons to be cheerful

Some students (not all) like this!! Groupwork works Shared media (meshes next?)