[3dem] 25 years of Situs: Spaghetti Tracer, Struwwel Tracer, and ElConDe

[Wriggers, Willy R.]

Dear 3DEM community,

On this day in 1999, I announced the first version of Situs on this mailing list. I did not know at that time that cryo-EM and tomography-based modeling would keep me and my computational group busy for my whole career, but here we are, 25 years later!

To celebrate the anniversary, we are rolling out a new version of Situs with cutting-edge tools for tracing filaments in 3D tomograms:

Spaghetti Tracer (fast tracing of semi-ordered filament bundles in tomograms)  [1]
Struwwel Tracer (fast tracing of random oriented filament networks in tomograms) [2], and
elConDe (template-constrained deconvolution of semi-ordered filaments) [3].

Please check out the software web site with details on the rollout: https://urldefense.com/v3/__https://situs.biomachina.org/__;!!Mih3wA!BL01bC5bg1GJBQ1jykwsO9g4plAjMa1kCGtoEDovCaFO6dmMkyd7zCdhaMzdb-eUiehNMvoa8DfAeYAfTwzw$ 

I would also like to dedicate this release to the memory of two students we lost over the years, my student Paul Boyle from Ireland, a Situs developer who passed away twenty years ago [4], and Manfred Auer's student Junha Song from South Korea, a coauthor of [3], who passed away last year (see acknowledgement/dedication in [2]). It has been a privilege and inspiration to work with them.

Best wishes for the next 25 years.
Willy

Willy Wriggers, Ph.D.
Frank Batten Chair of Mechanical and Aerospace Engineering
Old Dominion University
238 Kaufman Hall
Norfolk, Virginia 23529

[1] Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers. Spaghetti Tracer: A Framework for Tracing Semiregular Filamentous Densities in 3D Tomograms. Biomolecules 12 (8), 1022, 2022 https://urldefense.com/v3/__https://www.mdpi.com/2218-273X/12/8/1022__;!!Mih3wA!BL01bC5bg1GJBQ1jykwsO9g4plAjMa1kCGtoEDovCaFO6dmMkyd7zCdhaMzdb-eUiehNMvoa8DfAeZITSWyQ$ 
[2] Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers. Untangling Irregular Actin Cytoskeleton Architectures in Tomograms of the Cell with Struwwel Tracer. International Journal of Molecular Sciences 24 (24), 17183, 2023 https://urldefense.com/v3/__https://www.mdpi.com/1422-0067/24/24/17183__;!!Mih3wA!BL01bC5bg1GJBQ1jykwsO9g4plAjMa1kCGtoEDovCaFO6dmMkyd7zCdhaMzdb-eUiehNMvoa8DfAeZK2nLsh$ 
[3] Julio Kovacs, Junha Song, Manfred Auer, Jing He, Wade Hunter, Willy Wriggers. Correction of missing-wedge artifacts in filamentous tomograms by template-based constrained deconvolution. Journal of chemical information and modeling 60 (5), 2626-2633, 2020 https://urldefense.com/v3/__https://pubs.acs.org/doi/10.1021/acs.jcim.9b01111__;!!Mih3wA!BL01bC5bg1GJBQ1jykwsO9g4plAjMa1kCGtoEDovCaFO6dmMkyd7zCdhaMzdb-eUiehNMvoa8DfAeVQMNZDR$ 
[4] https://urldefense.com/v3/__https://w.biomachina.org/people/pboyle/__;!!Mih3wA!BL01bC5bg1GJBQ1jykwsO9g4plAjMa1kCGtoEDovCaFO6dmMkyd7zCdhaMzdb-eUiehNMvoa8DfAedJ4jz7Y$ 
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