A minor boast: it’s gratifying to see the hard work Dr. Roederer and I have done on SPICE is being put to good use. The paper has been cited* a number of times. This week I went back to work for Dr. Roederer full-time to continue improving SPICE and to plan and build yet another bioinformatics tool.
* I also just discovered Google Scholar. 
SPICE was cited in a paper published in the Journal of Virology this month.
Michael A. Eller,1,2,3,* Rebecca N. Koehler,3 Gustavo H. Kijak,3 Leigh Anne Eller,2,3 David Guwatudde,2,4 Mary A. Marovich,3 Nelson L. Michael,3 Mark S. de Souza,3,5 Fred Wabwire- Mangen,2,4 Merlin L. Robb,3 Jeffrey R. Currier,3 and Johan K. Sandberg,1
SPICE was published in the Wiley journal Cytometry on January 7, 2011 and is listed on the Vaccine Research Center’s list of 2011 publications.
SPICE: Exploration and analysis of post-cytometric complex multivariate datasets
Mario Roederer, Joshua L. Nozzi, Martha X. Nason
Cytometry
DOI: 10.1002/cyto.a.21015
Polychromatic flow cytometry results in complex, multivariate datasets. To date, tools for the aggregate analysis of these datasets across multiple specimens grouped by different categorical variables, such as demographic information, have not been optimized. Often, the exploration of such datasets is accomplished by visualization of patterns with pie charts or bar charts, without easy access to statistical comparisons of measurements that comprise multiple components. Here we report on algorithms and a graphical interface we developed for these purposes. In particular, we discuss thresholding necessary for accurate representation of data in pie charts, the implications for display and comparison of normalized versus unnormalized data, and the effects of averaging when samples with significant background noise are present. Finally, we define a statistic for the nonparametric comparison of complex distributions to test for difference between groups of samples based on multi-component measurements. While originally developed to support the analysis of T cell functional profiles, these techniques are amenable to a broad range of datatypes. Published 2011 Wiley-Liss, Inc.
SPICE is a product of NIH/NIAID and is hosted here: http://exon.niaid.nih.gov/spice
I had missed this (or, rather, Google Alerts had). AlphaVax had apparently given a presentation titled Flow-Cytometric Evaluation of T-Cell Responses Elicited by an Alphavirus Replicon Particle Vaccine for Cytomegalovirus (CMV) in Healthy Adults sometime in June.
Quite a mouthful. The presentation describes how AlphaVax used multiparameter flow cytometry to explore one of their vaccine candidates. They then used – among other applications – SPICE 5 to do their data mining, visualization, and production of presentation-quality graphs for their presentation.
Samples were fixed and stored at 4°C until acquisition on an LSRII flow cytometer. Flow data was analyzed with FlowJo version 8.7 (Tree Star, Ashland, OR). Further data analysis was performed using software (PESTLE and SPICE, version 5.0) provided by M. Roederer and J. Nozzi, NIAID, NIH.
It makes me proud to know my work is directly helping researchers find vaccines for “what ails ya.” Very gratifying.
Temporis was featured in the February issue of Mac|Life magazine in print and on the web.
The timeline app was given a very positive – if brief – mention. It’s nice to see it’s still loved a few years after its initial release. I had put a lot of polish into it.
Thanks to @salconigliaro for snapping the photo for me (I’m not a subscriber, sorry Mac|Life).
Today I was proud to stand with my colleagues and receive the 2009 National Institute of Allergy & Infectious Diseases Chief Information Officer Award for our hard work on the Papillomavirus Episteme (PaVE).
PaVE is a public-facing research tool for biologists researching the Papillomaviridae family of viruses. I was (and continue to be) the usability analyst and UI designer for the project. The team includes Yasmin Mohomoud, Vivek Gopalan, Sandya Bandaru, Qina Tan, Jason Barnett, and Yongjian (Jason) Guo, Leo (Li) Lu, as well as myself. Congratulations, all!
C. Montgomery Burns Voice: Ehhhxcellence.
Josh is a thirty-something Cocoa / Objective-C / Xcode developer and technical author living in the Baltimore / D.C. area. He loves his cats, his wine, his family, a quiet neighborhood, and a good book. Josh is a Cocoa developer for hire.
The views and opinions expressed here are my own and do not reflect those of my employers.
