MOTIVATIONParticle tracking coupled with time-lapse microscopy is critical for understanding the ... more MOTIVATIONParticle tracking coupled with time-lapse microscopy is critical for understanding the dynamics of intracellular processes of clinical importance. Spurred on by advances in the spatiotemporal resolution of microscopy and automated computational methods, this field is increasingly amenable to multi-dimensional high-throughput data collection schemes (Snijder et al., 2012). Typically, complex particle tracking datasets generated by individual laboratories are produced with incompatible methodologies that preclude comparison to each other. There is therefore an unmet need for data management systems that facilitate data standardization, meta-analysis, and structured data dissemination. The integration of analysis, visualization, and quality control capabilities into such systems would eliminate the need for manual transfer of data to diverse downstream analysis tools. At the same time, it would lay the foundation for shared trajectory data, particle tracking, and motion analy...
There has always been a strong relationship between chemists’ understanding of chemical phenomena... more There has always been a strong relationship between chemists’ understanding of chemical phenomena and the associated external representations. It is thus common wisdom that visualization tools should play a prominent role in the chemistry discovery cycle, and they do indeed. But looking at them with a non-chemist’s eye reveals that they implement some interesting visualization ideas, but fall short on the perceptual support side and, more important, on the implementation of human-computer interaction (HCI) ideas. In this work we substantiate those findings with a tool survey and an inventory of chemistry representation methods. We hope those two results will be the basis for engaging a discussion with the chemistry research community to clarify, understand and define the characteristics that an effective chemistry visualization tool should have.
... This is especially useful for calculations where we let many good structures from different f... more ... This is especially useful for calculations where we let many good structures from different funnels survive, thus ... This means that this fitness function depends on history of the simulation. ... Any method is worth as much as its applications are, and here we review only a small ...
Edward Tufte reminds us: "The world we seek to understand is multivariate". This is tru... more Edward Tufte reminds us: "The world we seek to understand is multivariate". This is true also in typical scientific fields, like chemistry and biology, where there are interesting data that do not live in usual three-dimensional spaces. Examples are all around us: genomic data live in the gene sequence space, drug discovery with their structure correlation methods, quantum chemistry and
MOTIVATIONParticle tracking coupled with time-lapse microscopy is critical for understanding the ... more MOTIVATIONParticle tracking coupled with time-lapse microscopy is critical for understanding the dynamics of intracellular processes of clinical importance. Spurred on by advances in the spatiotemporal resolution of microscopy and automated computational methods, this field is increasingly amenable to multi-dimensional high-throughput data collection schemes (Snijder et al., 2012). Typically, complex particle tracking datasets generated by individual laboratories are produced with incompatible methodologies that preclude comparison to each other. There is therefore an unmet need for data management systems that facilitate data standardization, meta-analysis, and structured data dissemination. The integration of analysis, visualization, and quality control capabilities into such systems would eliminate the need for manual transfer of data to diverse downstream analysis tools. At the same time, it would lay the foundation for shared trajectory data, particle tracking, and motion analy...
There has always been a strong relationship between chemists’ understanding of chemical phenomena... more There has always been a strong relationship between chemists’ understanding of chemical phenomena and the associated external representations. It is thus common wisdom that visualization tools should play a prominent role in the chemistry discovery cycle, and they do indeed. But looking at them with a non-chemist’s eye reveals that they implement some interesting visualization ideas, but fall short on the perceptual support side and, more important, on the implementation of human-computer interaction (HCI) ideas. In this work we substantiate those findings with a tool survey and an inventory of chemistry representation methods. We hope those two results will be the basis for engaging a discussion with the chemistry research community to clarify, understand and define the characteristics that an effective chemistry visualization tool should have.
... This is especially useful for calculations where we let many good structures from different f... more ... This is especially useful for calculations where we let many good structures from different funnels survive, thus ... This means that this fitness function depends on history of the simulation. ... Any method is worth as much as its applications are, and here we review only a small ...
Edward Tufte reminds us: "The world we seek to understand is multivariate". This is tru... more Edward Tufte reminds us: "The world we seek to understand is multivariate". This is true also in typical scientific fields, like chemistry and biology, where there are interesting data that do not live in usual three-dimensional spaces. Examples are all around us: genomic data live in the gene sequence space, drug discovery with their structure correlation methods, quantum chemistry and
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Papers by Mario Valle