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Showing 145 to 153 of 153 entries
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Iris: Interactive all-in-one graphical validation of 3D protein model iterations.

Protein science : a publication of the Protein Society

Rochira W, Agirre J.
PMID: 32964594
Protein Sci. 2021 Jan;30(1):93-107. doi: 10.1002/pro.3955. Epub 2020 Oct 19.

Iris validation is a Python package created to represent comprehensive per-residue validation metrics for entire protein chains in a compact, readable and interactive view. These metrics can either be calculated by Iris, or by a third-party program such as...

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Rochira W, Agirre J. Iris: Interactive all-in-one graphical validation of 3D protein model iterations. Protein Sci. 2020;30(1):93-107doi: 10.1002/pro.3955.
Rochira, W., & Agirre, J. (2021). Iris: Interactive all-in-one graphical validation of 3D protein model iterations. Protein science : a publication of the Protein Society, 30(1), 93-107. https://doi.org/10.1002/pro.3955
Rochira, William, and Agirre, Jon. "Iris: Interactive all-in-one graphical validation of 3D protein model iterations." Protein science : a publication of the Protein Society vol. 30,1 (2021): 93-107. doi: https://doi.org/10.1002/pro.3955
Rochira W, Agirre J. Iris: Interactive all-in-one graphical validation of 3D protein model iterations. Protein Sci. 2021 Jan;30(1):93-107. doi: 10.1002/pro.3955. Epub 2020 Oct 19. PMID: 32964594; PMCID: PMC7737763.
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Invisible Boundaries for VR: Auditory and Haptic Signals as Indicators for Real World Boundaries.

IEEE transactions on visualization and computer graphics

George C, Tamunjoh P, Hussmann H, Strickroth S.
PMID: 32941151
IEEE Trans Vis Comput Graph. 2020 Dec;26(12):3414-3422. doi: 10.1109/TVCG.2020.3023607. Epub 2020 Nov 10.

Maintaining awareness of real world boundaries whilst being immersed in virtual reality (VR) with head mounted displays (HMDs), is a necessity for the physical integrity of the user. This paper explores whether individual human senses can be allocated to...

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George C, Tamunjoh P, Hussmann H, et al. Invisible Boundaries for VR: Auditory and Haptic Signals as Indicators for Real World Boundaries. IEEE Trans Vis Comput Graph. 2020;26(12):3414-3422doi: 10.1109/TVCG.2020.3023607.
George, C., Tamunjoh, P., Hussmann, H., & Strickroth, S. (2020). Invisible Boundaries for VR: Auditory and Haptic Signals as Indicators for Real World Boundaries. IEEE transactions on visualization and computer graphics, 26(12), 3414-3422. https://doi.org/10.1109/TVCG.2020.3023607
George, Ceenu, et al. "Invisible Boundaries for VR: Auditory and Haptic Signals as Indicators for Real World Boundaries." IEEE transactions on visualization and computer graphics vol. 26,12 (2020): 3414-3422. doi: https://doi.org/10.1109/TVCG.2020.3023607
George C, Tamunjoh P, Hussmann H, Strickroth S. Invisible Boundaries for VR: Auditory and Haptic Signals as Indicators for Real World Boundaries. IEEE Trans Vis Comput Graph. 2020 Dec;26(12):3414-3422. doi: 10.1109/TVCG.2020.3023607. Epub 2020 Nov 10. PMID: 32941151.
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Visualization Equilibrium.

IEEE transactions on visualization and computer graphics

Kayongo P, Sun G, Hartline J, Hullman J.
PMID: 34587069
IEEE Trans Vis Comput Graph. 2022 Jan;28(1):465-474. doi: 10.1109/TVCG.2021.3114842. Epub 2021 Dec 24.

In many real-world strategic settings, people use information displays to make decisions. In these settings, an information provider chooses which information to provide to strategic agents and how to present it, and agents formulate a best response based on...

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Kayongo P, Sun G, Hartline J, et al. Visualization Equilibrium. IEEE Trans Vis Comput Graph. 2021;28(1):465-474doi: 10.1109/TVCG.2021.3114842.
Kayongo, P., Sun, G., Hartline, J., & Hullman, J. (2022). Visualization Equilibrium. IEEE transactions on visualization and computer graphics, 28(1), 465-474. https://doi.org/10.1109/TVCG.2021.3114842
Kayongo, Paula, et al. "Visualization Equilibrium." IEEE transactions on visualization and computer graphics vol. 28,1 (2022): 465-474. doi: https://doi.org/10.1109/TVCG.2021.3114842
Kayongo P, Sun G, Hartline J, Hullman J. Visualization Equilibrium. IEEE Trans Vis Comput Graph. 2022 Jan;28(1):465-474. doi: 10.1109/TVCG.2021.3114842. Epub 2021 Dec 24. PMID: 34587069.
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An extensively modified version of MolScript that includes greatly enhanced coloring capabilities.

Journal of molecular graphics & modelling

Esnouf RM.
PMID: 9385560
J Mol Graph Model. 1997 Apr;15(2):132-4, 112-3. doi: 10.1016/S1093-3263(97)00021-1.

Owing to its flexibility, MolScript has become one of the most widely used programs for generating publication-quality molecular graphics. Integration with the Raster3D package, to allow the production of photorealistic rendered images, has increased its popularity still further. However,...

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Esnouf RM. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J Mol Graph Model. 1997;15(2):132-4, 112-3doi: 10.1016/S1093-3263(97)00021-1.
Esnouf, R. M. (1997). An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. Journal of molecular graphics & modelling, 15(2), 132-4, 112-3. https://doi.org/10.1016/S1093-3263(97)00021-1
Esnouf, R M. "An extensively modified version of MolScript that includes greatly enhanced coloring capabilities." Journal of molecular graphics & modelling vol. 15,2 (1997): 132-4, 112-3. doi: https://doi.org/10.1016/S1093-3263(97)00021-1
Esnouf RM. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J Mol Graph Model. 1997 Apr;15(2):132-4, 112-3. doi: 10.1016/S1093-3263(97)00021-1. PMID: 9385560.
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MetaCrop 2.0: managing and exploring information about crop plant metabolism.

Nucleic acids research

Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker BH, Klapperstück M, Scholz U, Weise S.
PMID: 22086948
Nucleic Acids Res. 2012 Jan;40:D1173-7. doi: 10.1093/nar/gkr1004. Epub 2011 Nov 15.

MetaCrop is a manually curated repository of high-quality data about plant metabolism, providing different levels of detail from overview maps of primary metabolism to kinetic data of enzymes. It contains information about seven major crop plants with high agronomical...

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Schreiber F, Colmsee C, Czauderna T, et al. MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res. 2011;40:D1173-7doi: 10.1093/nar/gkr1004.
Schreiber, F., Colmsee, C., Czauderna, T., Grafahrend-Belau, E., Hartmann, A., Junker, A., Junker, B. H., Klapperstück, M., Scholz, U., & Weise, S. (2012). MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic acids research, 40D1173-7. https://doi.org/10.1093/nar/gkr1004
Schreiber, Falk, et al. "MetaCrop 2.0: managing and exploring information about crop plant metabolism." Nucleic acids research vol. 40 (2012): D1173-7. doi: https://doi.org/10.1093/nar/gkr1004
Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker BH, Klapperstück M, Scholz U, Weise S. MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res. 2012 Jan;40:D1173-7. doi: 10.1093/nar/gkr1004. Epub 2011 Nov 15. PMID: 22086948; PMCID: PMC3245004.
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QualDash: Adaptable Generation of Visualisation Dashboards for Healthcare Quality Improvement.

IEEE transactions on visualization and computer graphics

Elshehaly M, Randell R, Brehmer M, McVey L, Alvarado N, Gale CP, Ruddle RA.
PMID: 33048727
IEEE Trans Vis Comput Graph. 2021 Feb;27(2):689-699. doi: 10.1109/TVCG.2020.3030424. Epub 2021 Jan 28.

Adapting dashboard design to different contexts of use is an open question in visualisation research. Dashboard designers often seek to strike a balance between dashboard adaptability and ease-of-use, and in hospitals challenges arise from the vast diversity of key...

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Elshehaly M, Randell R, Brehmer M, et al. QualDash: Adaptable Generation of Visualisation Dashboards for Healthcare Quality Improvement. IEEE Trans Vis Comput Graph. 2021;27(2):689-699doi: 10.1109/TVCG.2020.3030424.
Elshehaly, M., Randell, R., Brehmer, M., McVey, L., Alvarado, N., Gale, C. P., & Ruddle, R. A. (2021). QualDash: Adaptable Generation of Visualisation Dashboards for Healthcare Quality Improvement. IEEE transactions on visualization and computer graphics, 27(2), 689-699. https://doi.org/10.1109/TVCG.2020.3030424
Elshehaly, Mai, et al. "QualDash: Adaptable Generation of Visualisation Dashboards for Healthcare Quality Improvement." IEEE transactions on visualization and computer graphics vol. 27,2 (2021): 689-699. doi: https://doi.org/10.1109/TVCG.2020.3030424
Elshehaly M, Randell R, Brehmer M, McVey L, Alvarado N, Gale CP, Ruddle RA. QualDash: Adaptable Generation of Visualisation Dashboards for Healthcare Quality Improvement. IEEE Trans Vis Comput Graph. 2021 Feb;27(2):689-699. doi: 10.1109/TVCG.2020.3030424. Epub 2021 Jan 28. PMID: 33048727.
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Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space.

Faraday discussions

Pavlov E, Taiji M, Scukins A, Markesteijn A, Karabasov S, Nerukh D.
PMID: 25340552
Faraday Discuss. 2014;169:285-302. doi: 10.1039/c3fd00159h. Epub 2014 Jun 17.

A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of...

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Pavlov E, Taiji M, Scukins A, et al. Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space. Faraday Discuss. 2014;169:285-302doi: 10.1039/c3fd00159h.
Pavlov, E., Taiji, M., Scukins, A., Markesteijn, A., Karabasov, S., & Nerukh, D. (2014). Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space. Faraday discussions, 169285-302. https://doi.org/10.1039/c3fd00159h
Pavlov, Evgen, et al. "Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space." Faraday discussions vol. 169 (2014): 285-302. doi: https://doi.org/10.1039/c3fd00159h
Pavlov E, Taiji M, Scukins A, Markesteijn A, Karabasov S, Nerukh D. Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space. Faraday Discuss. 2014;169:285-302. doi: 10.1039/c3fd00159h. Epub 2014 Jun 17. PMID: 25340552.
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The Virtual Kidney: an eScience interface and Grid portal.

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

Harris PJ, Buyya R, Chu X, Kobialka T, Kazmierczak E, Moss R, Appelbe W, Hunter PJ, Thomas SR.
PMID: 19414450
Philos Trans A Math Phys Eng Sci. 2009 Jun 13;367(1896):2141-59. doi: 10.1098/rsta.2008.0291.

The Virtual Kidney uses a web interface and distributed computing to provide experimental scientists and analysts with access to computational simulations and knowledge databases hosted in geographically separated laboratories. Users can explore a variety of complex models without requiring...

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Harris PJ, Buyya R, Chu X, et al. The Virtual Kidney: an eScience interface and Grid portal. Philos Trans A Math Phys Eng Sci. 2009;367(1896):2141-59doi: 10.1098/rsta.2008.0291.
Harris, P. J., Buyya, R., Chu, X., Kobialka, T., Kazmierczak, E., Moss, R., Appelbe, W., Hunter, P. J., & Thomas, S. R. (2009). The Virtual Kidney: an eScience interface and Grid portal. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, 367(1896), 2141-59. https://doi.org/10.1098/rsta.2008.0291
Harris, Peter J, et al. "The Virtual Kidney: an eScience interface and Grid portal." Philosophical transactions. Series A, Mathematical, physical, and engineering sciences vol. 367,1896 (2009): 2141-59. doi: https://doi.org/10.1098/rsta.2008.0291
Harris PJ, Buyya R, Chu X, Kobialka T, Kazmierczak E, Moss R, Appelbe W, Hunter PJ, Thomas SR. The Virtual Kidney: an eScience interface and Grid portal. Philos Trans A Math Phys Eng Sci. 2009 Jun 13;367(1896):2141-59. doi: 10.1098/rsta.2008.0291. PMID: 19414450.
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VBridge: Connecting the Dots Between Features and Data to Explain Healthcare Models.

IEEE transactions on visualization and computer graphics

Cheng F, Liu D, Du F, Lin Y, Zytek A, Li H, Qu H, Veeramachaneni K.
PMID: 34596543
IEEE Trans Vis Comput Graph. 2022 Jan;28(1):378-388. doi: 10.1109/TVCG.2021.3114836. Epub 2021 Dec 24.

Machine learning (ML) is increasingly applied to Electronic Health Records (EHRs) to solve clinical prediction tasks. Although many ML models perform promisingly, issues with model transparency and interpretability limit their adoption in clinical practice. Directly using existing explainable ML...

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Cheng F, Liu D, Du F, et al. VBridge: Connecting the Dots Between Features and Data to Explain Healthcare Models. IEEE Trans Vis Comput Graph. 2021;28(1):378-388doi: 10.1109/TVCG.2021.3114836.
Cheng, F., Liu, D., Du, F., Lin, Y., Zytek, A., Li, H., Qu, H., & Veeramachaneni, K. (2022). VBridge: Connecting the Dots Between Features and Data to Explain Healthcare Models. IEEE transactions on visualization and computer graphics, 28(1), 378-388. https://doi.org/10.1109/TVCG.2021.3114836
Cheng, Furui, et al. "VBridge: Connecting the Dots Between Features and Data to Explain Healthcare Models." IEEE transactions on visualization and computer graphics vol. 28,1 (2022): 378-388. doi: https://doi.org/10.1109/TVCG.2021.3114836
Cheng F, Liu D, Du F, Lin Y, Zytek A, Li H, Qu H, Veeramachaneni K. VBridge: Connecting the Dots Between Features and Data to Explain Healthcare Models. IEEE Trans Vis Comput Graph. 2022 Jan;28(1):378-388. doi: 10.1109/TVCG.2021.3114836. Epub 2021 Dec 24. PMID: 34596543.
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Showing 145 to 153 of 153 entries