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2017 / Annual report / Narrative / C. Titus Brown / Moore DDD Investigator

Progress

Describe your project's progress in the last year. Please reference your initial project objectives when possible.

Award purpose:

In support of demonstrating the high level of scientific impact that data scientists deliver through their focus on interdisciplinary data-driven research; funds from this award will be used to better understand gene function in non-model organisms through the development of new workflows and better data sharing technology for large-scale data analysis.

Essentially, our project is to explore discovery and semi-automated analyses of sequencing data, with the goal of eventually supporting large scale mining of correlations across All the Data. The challenge is that these are all underdeveloped technologies in non-model organism genomics.

The second year of my award saw substantial progress towards outlining a strategy towards these ends, and developing specific foundational technologies and software. (The first year of this award was dominated by the process of moving to UC Davis and recruiting postdocs to my new lab!) Since last report, three new postdocs (Daniel Standage, Harriet Alexander, and Phillip Brooks) have joined, and all are working on DDD-related projects.

We are now moving forward on several fronts:

  • we have a transcriptomics team working on reanalysis of 700 transcriptomes (MMETSP project, Lisa Cohen and Harriet Alexander) using technology developed by Camille Scott (dammit and shmlast). In addition to the primary products (new & better assemblies), we have a robust, quality-controlled open and canonical de novo assembly and annotation pipeline that can be applied to any eukaryotic RNAseq data set.

  • a metagenomics group (Sherine Awad, Phil Brooks) is moving towards the same goal in metagenomics data analysis.

  • our distributed/scalability tiger team (Luiz Irber) is working to build distributed indices of MinHash sketches to make it possible to find relevant data sets and analyses in public databases. As part of this Luiz is building a massively scalable indexing infrastructure that closely resembles a botnet.

  • our core software development efforts are proceeding again, with Daniel Standage leading khmer development and a consultant (Tim Head) contributing to development, code review, and testing.

  • while doing all of this, we continue to explore the landscape of tools and resources around notions of openness, repeatability, decentralization and distribution, and community engagement. In addition to my continuing social media postings, an analysis of challenges in doing large scale data reanalysis in a small lab will be submitted along with the primary MMETSP reanalysis paper.

  • an important component of all our work is our teaching and training effort, aimed at building a local community of practice around data-driven discovery while engaging with the global community being nucleated by the Data Science Environments and Data Carpentry. Towards this end we have run dozens of workshops in the past two years and plan to considerably scale up in the summer of 2017.

It's hard to predict where we will end up but I'm enjoying the ride, and in the meantime we are producing useful software products and doing interesting analyses.

Awareness and recognition

Describe evidence of awareness/recognition of you, your projects, and/or your lab members.

I continue to be recognized as a source of informed opinion about issues of open science, computational infrastructure, scientific software engineering, and repeatability/reproducibility. The primary broadcast medium for these opinions is social media, with my blog and Twitter accounts. As evidence of engagement, my blog sees about 90,000 page views a year, and gathers about 200 comments per year; I don't know how to summarize my Twitter traffic. It seems likely that many of my invitations and advisory board memberships come from my social media presence, as I have mostly avoided publishing opinion pieces or review articles in traditional locations. I also routinely provide background information and give interviews to science journalists.

More than just me, the lab is increasingly being recognized as a source of expertise in software development, data-intensive research, and infrastructure. For example, Luiz did a tutorial on Docker at Supercomputing 2016; Harriet and Daniel both participated in a national Plant Biology computing infrastructure visioning workshop; and Harriet has participated in several additional visioning workshops and grant review panels.

Expenditures

The large majority of my expenditures are on personnel - postdocs and grad students. This past year saw the arrival of postdocs Harriet Alexander and Phil Brooks, as well as continuing support for Sherine Mahmoud, Camille Scott, and Luiz Irber. Because Harriet and Phil took longer to arrive than planned, I underspent for the year by about 17% on personnel.

The "supplies and expenses" line item was off by more than 20% - this was because I had two big expenses: I hired Tim Head as a software engineer contractor (approximatel $15k, and I put down 1/4 of an order for an Oxford Nanopore Promethion instrument that will arrive soon.

Help requested

Compute infrastructure

There is a general confusion and lack of clarity around the computational infrastructure needs of Data Driven Discovery, and where and how to meet them. This includes just-in-time resources for training, long term storage of large datasets, "scale out" technology options, good-enough practice in making use of the options, and funding/support for large scale compute and storage. (This is also alluded to in Casey Greene's report.)

We are working on a local (UC Davis School of Vet Med) solution to container hosting, and also starting to interact more closely with NSF's JetStream, as two possible solutions for our lab.

But, more generally, I don't know what a sustainable option is here. It seems like a good opportunity for some brainstorming.

Learning about deep learning

I need to know more about deep learning, and gain some hands on experience. More, I would like to be able to engage closely with experts in order to figure out what will and won't work. People in my lab are also interested in this. Where do we go?