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59 changes: 52 additions & 7 deletions src/constants/networked-trajectories.ts
Original file line number Diff line number Diff line change
Expand Up @@ -193,7 +193,6 @@ const TRAJECTORIES: TrajectoryDisplayData[] = [
imageFile: medyan2Image,
gifFile: medyan2Gif,
},
/*
{
modelName: "Vivarium E coli",
id: "vivarium_ecoli.simularium",
Expand All @@ -206,15 +205,16 @@ const TRAJECTORIES: TrajectoryDisplayData[] = [
year: 2020,
url: "https://www.mdpi.com/1099-4300/22/10/1101",
},
description: "Model of chemotactic E. coli using Vivarium.",
description:
"A multiscale model of chemotactic E. coli built using Vivarium.",
code:
"Software used to generate this data is available <a href='https://github.com/vivarium-collective/vivarium-chemotaxis'>here</a>.",
legalese:
thirdPartyLicensing("https://github.com/vivarium-collective/vivarium-chemotaxis/blob/master/LICENSE"),
imageFile: vivariumImage,
gifFile: vivariumGif,
legalese: thirdPartyLicensing(
"https://github.com/vivarium-collective/vivarium-chemotaxis/blob/master/LICENSE"
),
imageFile: "",
gifFile: "",
},
*/
{
modelName: "Condensate Formation",
id: "springsalad_condensate_formation_Below_Ksp.simularium",
Expand Down Expand Up @@ -335,6 +335,51 @@ const TRAJECTORIES: TrajectoryDisplayData[] = [
imageFile: listeriaUltrapolarImage,
},
*/
{
modelName: "Blood Plasma",
id: "blood-plasma-1.0.simularium",
title: "Blood Plasma",
totalSimulatedTime: "0s",
version: "1.0",
authors:
"Graham T Johnson, Ludovic Autin, Mostafa Al-Alusi, David S Goodsell, Michel F Sanner & Arthur J Olson",
publication: {
title:
"cellPACK: a virtual mesoscope to model and visualize structural systems biology",
journal: "Nature Methods",
year: 2015,
url: "https://www.nature.com/articles/nmeth.3204",
},
description:
"A cellPACK model of a 100 nm × 100 nm × 15 nm volume of human blood plasma based on a mesoscale recipe containing information for the most abundant macromolecules.",
code:
"Software used to generate this data is available <a href='https://github.com/mesoscope/cellpack'>here</a>.",
legalese: thirdPartyLicensing(
"https://github.com/mesoscope/cellpack/blob/main/LICENSE"
),
imageFile: "",
gifFile: "",
},
{
modelName: "Red Blood Cell Cytoskeleton during Malaria Infection",
id: "readdy_malaria.simularium",
title: "Red Blood Cell Cytoskeleton during Malaria Infection",
totalSimulatedTime: "200 μs",
authors: "Julia Jäger et al",
publication: {
title:
"A particle-based computational model to analyse remodelling of the red blood cell cytoskeleton during malaria infections",
journal: "PLOS Computational Biology",
year: 2022,
url:
"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009509",
},
description: "",
code:
"Software used to generate this data is available <a href='https://github.com/usschwarz/networks'>here</a>.",
imageFile: "",
gifFile: "",
},
];

export default TRAJECTORIES;