INFORMATICS FOR THE SCIENCES continued
Displays and human interface Dr. Richard Scheuermann of the J. Craig Venter Institute (La Jolla, CA) de-
scribed a complex process for upgrading masses of biodata to knowledge. Ontologies help organize data from different files. Graph and statistical analysis of the data files supports generation of semantic assertions. The process uses 288 parallel pipelines. Data are organized by clustering using a variety of visuals including Venn diagrams supported by complex annotated tables. Dr. Scheuermann quickly discussed improved visual presentation of outputs from a fluorescence activated cell sorter. While these were improvements over conventional displays, it is clear that more creativity in data display would certainly help. Dr. Scott Kahn of Illumina (San Diego, CA) also cited this need and opportunity.
Semantic searches often produce complex graph visual displays, re- ferred to by several lecturers as (feline) “fur balls.” The problem is how to visualize a multidimensional relationship in two dimensions. Color, line width, and internodal distance are all used, but displays can still be incomprehensible and often unreadable. New designs for the human interface for complex, data-rich relationships are needed.
Energy consumption Server farms use huge amounts of energy. One estimate is that in 2012,
server farms consumed about as much energy as the commercial air- lines. This is about 2% of the global energy consumption. However, the doubling time of information is less than two years. If this continues for a decade, the extrapolated energy consumption could be 25
(32×) to 26
(64×). This forecast is probably not sustainable. But what will give? Will new energy-efficient computer technology sweep in?
Genomics: Do we even know what we do not know? Genomics will certainly involve curating and interrogating very large
databases. Prof. Eric Topol (Scripps Clinic, San Diego, CA) urges digitizing everyone. He adds that it is not the tumor location but the mutation that is relevant to cancer diagnosis and therapy. In a few cases, this works.
However, our understanding of genomics does not yet give an adequate picture of cancer’s etiology. “Junk DNA” is no longer junk. Circulating tumor cells (CTCs) indicate cancer, but when individual cells are se- quenced, the DNA is very heterogeneous. Which mutation should be targeted? Solid tumor masses show similar heterogeneity. CTCs and bi- opsies are probably useful in diagnosis, but how should we use the result prognostically? Then, what about exogenous RNA and epigenetics? It is clear that we have a lot to learn.
Credits The Molecular Med Tri-Con 2014 attracted 3200 scientists to San Francisco’s Moscone Convention Center from February 9 to 14 for an intense, multifaceted program split into 22 tracks covering a range of topics. The exhibition also provided an opportunity for multidisciplinary scientists to see product and service offerings. Three of the tracks dealt with modern data management. I want to congratulate Ms. Cindy Crowninshield, Director of Pharmaceutical Strategy at Cambridge Healthtech Institute (Needham, MA), for organizing the outstanding technical and support program for the informatics tracks.
Molecular Med Tri-Con 2015 will take place February 15–20 in San Francisco. For information, visit
http://www.triconference.com/.
References 1.
http://www.americanlaboratory.com/913-Technical-Articles/138841- sbv-IMPROVER-Species-Translation-Challenge-Open-to-the-Scientific- Community-for-Submissions/.
2.
http://www.americanlaboratory.com/913-Technical-Articles/149618- Results-are-in-for-the-Second-sbv-IMPROVER-Challenge-on-Species- Translation/.
Robert L. Stevenson, Ph.D., is Editor, American Laboratory/Labcompare; e-mail:
rlsteven@yahoo.com.
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