Software Engineer TBN, 0.6 Cal Months. One of the lab's four programmers or software engineers will work to improve the robustness of software and facilitate interactions with the CZI group. The programmer will provide code review, assistance with software engineering questions, and will help the primary authors of source code on the project (Greg, Qiwen, and Jaclyn) develop source code that is ready for handover to the CZI Engineering team as circumstances warrant.
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Computing (AWS, Google, or equivalent). $5000. We will be processing and analyzing known datasets, as well as evaluation datasets to be determined from the HCA. This budget is designed to support bootstrap estimates of transcript abundances from a modestly sized HCA benchmark kit plus pre- and post-processing required after model training. We expect that analysis of compendia of HCA data that are too large for this budget, including bootstrap analysis and preprocessing, would be handled directly by CZI.
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Graphics Cards (6GB 1060 or similar). $1500. We have already purchased access to a set of GPU computing machines at Penn that will be available for the duration of this grant. However, we expect to add mid-range GPUs to our existing desktop machines so that each member of the project team can run test code on their local machines for small proof-of-concept experiments.
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Travel (2 x 1-day Bay Area Meetings). $3500. This will fund the PI's travel to the SF Bay Area for two one-day in person discussions related to this grant.
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CZI Engineering (Not Budgeted) We will not, under this application, plan to develop software intended for broad use. In the event that we develop methods that are suitable for broad application, we hope to work with the engineering team at CZI to produce software for this purpose. To make sure that CZI engineers will be working with well-structured proof-of-concept code, we perform code review of our analytical code. We have also budgeted a very modest commitment from a professional programmer to aid in these efforts.