ORCID: 0000-0002-0764-4090
Research Interests: bioinformatics, computational biology, high-performance computing, visualization
Positions
| 2014—present | Director of Data Science | Computing and Information Services, Brown University |
| 2014—2015 | Interim Executive Director | Center for Computation and Visualization, Brown University |
| 2010—2014 | Application Scientist | Center for Computation and Visualization, Brown University |
| 2008—2010 | Computer Systems Engineer | Visualization Group, Lawrence Berkeley National Lab |
Education
| 2009 | M.S. Computer Science | University of California, Berkeley |
| 2006 | B.S. Mathematics | Brown University |
Research Projects
Sequence Assembly, Dunn Lab & Edwards Lab
I'm leading a research project into statistical methods for de novo sequence assembly and assessment. We recently created GABI, a prototype of a Bayesian genome assembler. Our goals are to perform Bayesian inference of splice variants during transcriptome assembly of RNAseq data, and to perform Bayesian genome assembly of chloroplast genomes that (surprisingly) cannot be resolved from high-coverage Illumnina data into single contigs by any existing assembly method.
Phylogenomic Analysis, Dunn Lab
We have developed Agalma, an automated workflow for transcriptome assembly and phylogenomic analysis of non-model species. I am also contributing to research into better methods for phylogenomic matrix construction. To automate these analyses, I developed BioLite, a bioinformatics framework that collects diagnostics and tracks provenance.
Software
| Bioinformatics Brew | a cross-platform package manager for bioinformatics tools |
| GABI | prototype of a Bayesian framework for genome sequence assembly |
| Agalma | automated transcriptome assembly and phylogenomics workflow |
| BioLite | bioinformatics framework in Python/C++ with automated tracking of diagnostics and provenance |
| SeqDB | storage model for Next Generation Sequencing data |
| PyModules | modules system for managing software environments on research computing clusters |
| GD3D | GPU-accelerated implementation of three commonly used 3D image denoising methods: bilateral filtering, anisotropic diffusion, and non-local means |
| Iota | lightweight tracing tool for diagnosing poorly performing I/O operations to parallel file systems, especially Lustre |
| H5Part | high-performenace, parallel I/O library in C for particle physics simulations |
| jmEscher | constrained Delauney triangulation library in Java using adaptive-precision arithmetic for robustness |
| WiiKinemathics | WiiRemote-enabled learning tool that uses gesture to teach 5th graders about proportion and ratio |
Publications
Bioinformatics & Computational Biology
Guang A, Zapata F, Howison M, Lawrence CE, Dunn CW. 2016. An Integrated Perspective on Phylogenetic Workflows. Trends in Ecology & Evolution 31(2): 116-126. doi:10.1016/j.tree.2015.12.007
Zapata F, Goetz F, Smith S, Howison M, et al. 2015. Phylogenomic Analyses Support Traditional Relationships within Cnidaria. PLOS ONE 10(10): e0139068. doi:10.1371/journal.pone.0139068
Howison M, Shen A. 2015. Bioinformatics Brew: the cross-platform package manager for open-source bioinformatics tools. Poster presented at Bio-IT World, 21-23 April 2015, Boston, MA, USA. doi:10.7301/Z0Z60KZD
Zapata F, Wilson NG, Howison M, et al. 2014. Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. Proc. R. Soc. B 281(1794): 20141739. doi:10.1098/rspb.2014.1739
Howison M, Zapata F, Edwards EJ, Dunn CW. 2014. Bayesian Genome Assembly and Assessment by Markov Chain Monte Carlo Sampling. PLoS ONE 9(6): e99497. doi:10.1371/journal.pone.0099497
Howison M, Zapata F, Dunn CW. 2013. Toward a statistically explicit understanding of de novo sequence assembly. Bioinformatics 29(23): 2959–2963. doi:10.1093/bioinformatics/btt525
Dunn CW, Howison M, Zapata F. 2013. Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14(1): 330. doi:10.1186/1471-2105-14-330
Howison M. 2013. High-throughput compression of FASTQ data with SeqDB. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10(1): 213-218. doi:10.1109/TCBB.2012.160
Howison M, Sinnott-Armstrong NA, Dunn CW. 2012. BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance. In Proceedings of the 4th USENIX Workshop on the Theory and Practice of Provenance (TaPP '12), 14-15 June 2012, Boston, MA, USA.
High-Performance Computing
Howison M, Prabhat, Byna S. 2014. Iota. In High Performance Parallel I/O, Chapman & Hall/CRC Computational Science, pp. 317-321.
Howison M, Bethel EW. 2014. GPU-accelerated denoising of 3D magnetic resonance images. Journal of Real-Time Image Processing. doi:10.1007/s11554-014-0436-8
Howison M, Shen A, Loomis A. 2013. Building Software Environments for Research Computing Clusters. In Proceedings of the 27th Large Installation System Administration Conference (LISA '13), 3-8 November 2013, Washington, DC, USA.
Bethel EW, Howison M. 2012. Multi-core and many-core shared-memory parallel raycasting volume rendering optimization and tuning. International Journal of High Performance Computing Applications 26(4): 399-412. doi:10.1177/1094342012440466
Howison M, Bethel EW, Childs H. 2012. Hybrid Parallelism for Volume Rendering on Large-, Multi-, and Many-Core Systems. IEEE Transactions on Visualization and Computer Graphics 18(1): 17-29. doi:10.1109/TVCG.2011.24
Howison M, Koziol Q, Knaak D, Mainzer J, Shalf J. 2010. Tuning HDF5 for Lustre File Systems. In Workshop on Interfaces and Abstractions for Scientific Data Storage (IASDS '10), 20-24 September 2010, Heraklion, Crete, Greece.
Howison M, Adelmann A, Bethel EW, Gsell A, Oswald B, Prabhat. 2010. H5hut: A High-Performance I/O Library for Particle-based Simulations. In Workshop on Interfaces and Abstractions for Scientific Data Storage (IASDS '10), 20-24 September 2010, Heraklion, Crete, Greece. doi:10.1109/CLUSTERWKSP.2010.5613098
Childs H, Pugmire D, Ahern S, Whitlock B, Howison M, Prabhat, Weber GH, Bethel EW. 2010. Extreme Scaling of Production Visualization Software on Diverse Architectures. IEEE Computer Graphics and Applications 30(3): 22–31. doi:10.1109/MCG.2010.51
Howison M, Bethel EW, Childs H. 2010. MPI-hybrid Parallelism for Volume Rendering on Large, Multi-core Systems. In Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization, 2-3 May 2010, Norrköping, Sweden. doi:10.2312/EGPGV/EGPGV10/001-010
Uselton A, Howison M, Wright NJ, Skinner D, Keen N, Shalf J, Karavanic KL, Oliker L. 2010. Parallel I/O performance: From events to ensembles. In Proceedings of the 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS), 19-23 April 2010, Atlanta, GA, USA. doi:10.1109/IPDPS.2010.5470424
Howison M. 2010. Comparing GPU Implementations of Bilateral and Anisotropic Diffusion Filters for 3D Biomedical Datasets. Paper presented at the SIAM Conference on Imaging Science (IS '10), 12-14 April 2012, Chicago, IL, USA. Technical Report LBNL-3425E.
Education & Artwork
Howison M, Trninic D, Reinholz D, Abrahamson D. 2011. The Mathematical Imagery Trainer: From Embodied Interaction to Conceptual Learning. In Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (CHI '11), pp. 1989–1998, 7-12 May 2011, Vancouver, BC, Canada. doi:10.1145/1978942.1979230
Abrahamson D, Howison M. 2010. Kinemathics: exploring kinesthetically induced mathematical learning. Paper presented at the annual meeting of the American Educational Research Association, 30 April - 4 May 2010, Denver, CO, USA.
Howison M, Séquin CH. 2009. CAD Tools for the Construction of 3D Escher Tiles. Computer-Aided Design and Applications 6(6): 737-748. doi:10.3722/cadaps.2009.737-748
3D Escher Tiles
For my master's degree, I designed and implemented CAD tools for creating decorative solids that tile 3-space in a regular, isohedral manner. These 3D tilings come in two flavors. The simpler method is to extrude and offset a 2D tiling. These are more like 2.5D tilings:
The second method is to derive true 3D tilings from cubic lattices:
This work involved several interesting algorithmic problems. To create offset 2.5D tilings, I designed an algorithm for cutting Delaunay triangulations by an arbitrary Jordan polygon. I also improved an existing algorithm for Delaunay triangulation (Lawson's incremental algorithm) by tuning its search heuristic to use the inherent symmetry of the tiles, and by applying adaptive-precision arithmetic to solve issues with numerical robustness. While developing these algorithms, I also invented visual debugging methods to overcome the difficulties of inspecting geometric data with standard text-based debuggers.
For full details, see my master's thesis:
Howison M. 2009. CAD Tools for Creating Space-filling 3D Escher Tiles (Master's thesis). University of California, Berkeley. UCB/EECS-2009-56.
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