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<div><b><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">**************</span></b></div>
<div><b><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">IAP/Spring</span></b></div>
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<p class="MsoNormal" style="margin: 15.95pt 0in;"><b><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">UROP Department, Lab or Center: Biology (Course 7)<o:p></o:p></span></b></p>
<p class="MsoNormal" style="margin: 15.95pt 0in;"><b><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">MIT Faculty Supervisor Name: Joey Davis<o:p></o:p></span></b></p>
<p class="MsoNormal" style="margin-bottom: 22.5pt;"><b><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">Project Title: </span></b><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">Accelerating
proteomics data analysis using highly parallel GPU-based processing<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom: 22.5pt; text-align: justify;"><b><span style="font-size:12.0pt;font-family:"Times New Roman";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"">Project Description: </span></b><span style="font-size:12.0pt;font-family:"Times New Roman";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"">High
resolution mass analysis of proteins and peptides reveals complex spectra that must be accurately fit to determine the relative abundance of analytes. This fitting process is computationally intensive, but is readily amenable to parallelization using modern
graphic processing units (GPUs). In this project, we will implement a least-squares Fourier transform convolution algorithm in CUDA and apply this algorithm to the analysis of a variety of mass spectra generated in our laboratory. The project includes the
following aspects: <o:p></o:p></span></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoNormal" style="margin-top: 3.75pt; margin-bottom: 3.75pt;"><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">Implementation of a fitting algorithm
on GPU hardware<o:p></o:p></span> </li><li class="MsoNormal" style="margin-top: 3.75pt; margin-bottom: 3.75pt;"><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">Use of a top-of-the-line mass spectrometer
to generate reference mass spectra for analysis<o:p></o:p></span> </li><li class="MsoNormal" style="margin-top: 3.75pt; margin-bottom: 3.75pt;"><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">Application of this fitting algorithm
to the quantitation of spectra generated above<o:p></o:p></span> </li><li class="MsoNormal" style="margin-top: 3.75pt; margin-bottom: 3.75pt;"><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">Analysis of the benefits of GPU-based
processing over traditional CPU-based implementations.<o:p></o:p></span> </li></ol>
<p class="MsoNormal" style="margin: 3.75pt 0in;"><span style="font-size:12.0pt;
font-family:"Times New Roman";mso-fareast-font-family:"Times New Roman";
mso-bidi-font-family:"Times New Roman""> </span></p>
<p class="MsoNormal" style="margin: 3.75pt 0in; text-align: justify;"><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">This UROP is offered in the Biology department,
however highly motivated applicants from departments such as Electrical Engineering & Computer Science, Mathematics, and Biological Engineering are encouraged to apply. While this UROP is primarily computational, students interested in learning more about
mass spectrometry will have significant opportunities to work in the wet laboratory. This UROP project will be directly supervised by Prof. Joey Davis.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin: 3.75pt 0in; text-align: justify;"><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman""> </span></p>
<p class="MsoNormal" style="margin-bottom: 22.5pt; text-align: justify;"><b><span style="font-size:12.0pt;font-family:"Times New Roman";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"">Prerequisites:</span></b><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman""> Candidates
of all experience levels will be considered. However, preference is given to candidates with experience with CUDA and/or python who can commit to working at least 20 hours per week during IAP and summer and 9 hours per week during the academic year. I am offering
academic credit for new UROPs.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom: 22.5pt;"><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">This project is expected to require IAP/Spring terms for completion,
however the UROP can be expanded to include additional projects in the coming years.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom: 22.5pt;"><b><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">Relevant URL:</span></b><span style="font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman""> </span><a href="http://www.jhdavislab.org"><span style="font-size:12.0pt;font-family:
"Times New Roman";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman"">www.jhdavislab.org</span></a><span style="font-size:12.0pt;
font-family:"Times New Roman";mso-fareast-font-family:"Times New Roman";
mso-bidi-font-family:"Times New Roman""><o:p></o:p></span></p>
<b><span style="font-size:12.0pt;line-height:107%;font-family:"Times New Roman";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA">Contact: </span></b><span style="font-size:12.0pt;line-height:107%;font-family:"Times New Roman";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA">Joey
Davis, <a href="mailto:jhdavis@mit.edu">jhdavis@mit.edu</a></span><!--EndFragment-->
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