Figma for Science

Avivator

There might be a big startup opportunity with porting old, widely used scientific tools to the web with Figma-like realtime annotation and rendering capabilities.

Scientific tooling is old but collaboration's more important than ever.

Realtime thinking is important. Beautiful rendering is important.

There might be a common toolkit that builds figma-like tools and can be turned bespoke for particular domains. Widgets for different kinds of data displays and manipulation. Jupyter/Julia notebook style.

I’m especially interested in cell stains/histology/pathology because microscopy is gorgeous to look at, and seems underexplored.

https://axial.substack.com/p/axial-benchling

Existing work:

(Benchling)

• Benchling
  • https://www.benchling.com/primers/
• HASH
• FloydHub
• Streamlit
• NextJournal
• Biodock
• ScienceIO
• https://blockpad.net/
• https://getluminal.com/
• https://www.colabra.app/
• https://latchbio.substack.com/p/crispr-bioinformatics-in-the-browser
• https://latch.bio
• BenchSci
• https://kanobo.com/
• https://www.microns-explorer.org/cortical-mm3
• https://riboviz.org
• https://www.paige.ai
• https://www.openmicroscopy.org/omero/
• https://synbiohub.org
• https://www.radix.bio/
• https://simularium.allencell.org
• https://czid.org
• http://vis.nucleome.org/entry/examples
• https://www.jkanche.com/kana/
• https://pathpresenter.net/login
• https://pathcore.com/live
• https://twitter.com/michaellee04/status/1557738197068656640?s=21&t=ymJUaWO2ZBrj4HCj9oFDxQ
• https://www.byterat.io/

(Biodock)

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"Experiment tracking" is a common theme

What if open science framework caught up with the times?

Journal of Open Research Software

Data to Discovery

An instance of Figma for X. Or maybe Palantir for X.

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Local-only systems (figma-izable)

Geology/Space

• https://github.com/cmudig/pixlise-c

Neuro

• https://github.com/MouseLand/receptivefield-explorer
• https://twitter.com/tomasfiers/status/1010580586208153600?s=21
• https://mne.tools/stable/index.html
• SimBrain
• https://surfer.nmr.mgh.harvard.edu/
• FSL
• https://www.janelia.org/lab/stringer-lab

Imagery

(Vizarr)

• Vizarr

• https://imagej.nih.gov/ij/docs/guide/146-8.html

• https://fiji.sc

• http://www.imagejfx.net/

• Bioformats - interop https://docs.openmicroscopy.org/bio-formats/6.8.1/about/index.html

• https://www.osirix-viewer.com/osirix/osirix-md/

• http://www.dicompyler.com

• ImageTwin (duplicate recognition) https://imagetwin.ai

Flow Cytometry

• https://www.flowjo.com/solutions/flowjo ($2000, on a dongle!)
• https://floreada.io/flow-cytometry-software
• https://www.beckman.com/flow-cytometry/software

Histology

The problem with microscopy is that file sizes are huge. Pathology/Histology is more tractable.

• https://www.histosearch.com

• https://qupath.github.io/

• ????

Informatics

Huge list here https://blog.addgene.org/free-online-molecular-biology-tools

https://phage.directory/tools

• https://bioconductor.org

• https://edinburgh-genome-foundry.github.io/

Abstract Viz

• https://centuryofbio.substack.com/p/visualizing-cellular-trajectories

Genomes

(Biocyc)

• https://biocyc.org
• https://jbrowse.org/jb2/
• http://gmod.org/wiki/GBrowse
• https://genomearchitect.readthedocs.io/en/latest/
• https://paintshop.io
  • R plugin
• https://github.com/cov-lineages/pangolin
• https://biowasm.com
• https://aidenlab.org/juicebox/
• http://www.celavi.pro
• https://pangenome.github.io/
• https://higlass.io/about

Primers

• https://dev.primer3plus.com/index.html

Synthetics

• https://async.ece.utah.edu/tools/ibiosim/
• http://synbiocad.org
• http://cellocad.org/#/welcome?redirect=%2Fhome

Plasmid Editing

Great overview: https://medium.com/@alice.menglh/may-7th-13th-8ab68cbc9e7b

• https://www.snapgene.com
• http://serialbasics.free.fr/Serial_Cloner.html
• https://jorgensen.biology.utah.edu/wayned/ape/
  • https://www.youtube.com/watch?v=98qtO-H9mLU
• Open Vector Editor (https://github.com/TeselaGen/ove-electron)
• SeqViz (just a viewer) https://github.com/Lattice-Automation/seqviz
• https://www.geneious.com
• https://www.nucleobytes.com/enzymex/index.html

Protein/Mol Sim

Molecular Viz

• Gelbox
• http://cadnano.org
• http://crystalmaker.com
• CellPAINT
• https://pymol.org/2/
• http://www.yasara.org
• https://www.cgl.ucsf.edu/chimera/download.html
• "Blender for Biochemists"
• https://aip.scitation.org/doi/full/10.1063/1.5039473?Track=APLBJUN20
• http://iqmol.org
• https://clarafi.com/training/intro-mmaya-dsdna-kit/

Sim

• https://en.m.wikipedia.org/wiki/ORCA_(quantum_chemistry_program)

Ligand Docking

• https://vina.scripps.edu
• https://en.wikipedia.org/wiki/List_of_protein-ligand_docking_software

In general, many domain specific tools are MATLAB plugins.

Molecule design

• https://optibrium.com/stardrop/

Misc

• https://www.kitware.com/platforms/

• Praat

• RCSB's PDB "view"s are crucial

• https://www.rcsb.org/3d-view/4hhb/1

  • https://www.rcsb.org/sequence/4Z35
  • https://www.rcsb.org/genome/4XVQ

• https://www.ncbi.nlm.nih.gov/structure

• https://www.czbiohub.org/technology-platforms/

• http://www.liheng.org/sw.shtml

• http://blog.booleanbiotech.com/computational-tools-2022.html

DSP Notebook

Graphics

Because all rendering of high-bit depth #bioimage data is done via #WebGL shaders directly in the browser, Viv applies data transformations without lag. Magic lenses that perform local transformations are smooth and changes to the color mapping update as sliders are moved. pic.twitter.com/7AFD5cWObX

— Nils Gehlenborg (@ngehlenborg) August 13, 2020

Open source ethics

Data should be easy to sync to a repo in a common format

Really what's being provisioned is the collaboration tool and hosting. Reasonable to charge a price that would otherwise require on prem and manual setup (and social features/external sharing!)

—-

https://newscience.org/how-software-in-the-life-sciences-actually-works-and-doesnt-work/

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Children

1. DSP Notebook

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Backlinks

• Organic Chemistry if it was Fun
• IDE/Photoshop/DAW for X
• Becoming a Resident Toolbuilder