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    <title>Computational Biology / Biological Computing</title>
    <link>https://computingbiology.github.io/</link>
    <description>Recent content on Computational Biology / Biological Computing</description>
    <generator>Hugo -- gohugo.io</generator>
    <language>en-us</language>
    <managingEditor>evans@virginia.edu (David Evans)</managingEditor>
    <webMaster>evans@virginia.edu (David Evans)</webMaster>
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    <item>
      <title>Final Project Submission</title>
      <link>https://computingbiology.github.io/final-project-submission/</link>
      <pubDate>Mon, 05 Dec 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/final-project-submission/</guid>
      <description>The form for submitting your final project is here: Final Project Artifact Submission Form
You should submit your final project by Tuesday, Dec 6 (AoE), which is 7:00am Eastern Time on Wednesday, Dec 7 (there is a 4 hour grace period on this, so you can submit up to 11:00am Wednesday, Dec 7 without any need to arrange an extension).
Note: this is different from the form you should use to submit your presentation: Project Presentation Form (as mentioned here).</description>
    </item>
    
    <item>
      <title>Class 24: Project Presentations and Covid Origins</title>
      <link>https://computingbiology.github.io/class24/</link>
      <pubDate>Thu, 01 Dec 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class24/</guid>
      <description>Slides: Class 24: Project Presentations and Covid Origins
  Letter organized by Peter Daszak, Statement in support of the scientists, public health professionals, and medical professionals of China combatting COVID-19, The Lancet, 19 February 2020. Addendum on competing interests, 21 June 2021.
  Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes and Robert F. Garry . The proximal origin of SARS-CoV-2. Nature Medicine, 17 March 2020.</description>
    </item>
    
    <item>
      <title>Quiz 3</title>
      <link>https://computingbiology.github.io/quiz-3/</link>
      <pubDate>Thu, 01 Dec 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/quiz-3/</guid>
      <description>Quiz 3 is posted here: Quiz 3
The quiz is untimed (no time limit enforced), but is expected to take about 30 minutes.
Before taking the quiz, make sure you understand and are confident you are able to follow the honor policy for this quiz:
  The quiz is closed resources. Once you start the quiz, you are not allowed to use any other materials. You should not switch to other browser tabs or look at any notes.</description>
    </item>
    
    <item>
      <title>Class 23: Protein Structure Prediction</title>
      <link>https://computingbiology.github.io/class23/</link>
      <pubDate>Tue, 29 Nov 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class23/</guid>
      <description>Schedule See the Schedule for Presentations and a Plan for this week on the github discussions site.
Slides and Links Slides: Class 23: Protein Structure Prediction (without annotations, will be updated later)
  Ken A. Dill, S. Banu Ozkan, M. Scott Shell, and Thomas R. Weikl. The Protein Folding Problem. Annual Review of Biophysics, 2008.
  Bonnie Berger and Tom Leighton. Protein Folding in the Hydrophobic-Hydrophilic Model is NP-Complete.</description>
    </item>
    
    <item>
      <title>Plans for Week and Presentations</title>
      <link>https://computingbiology.github.io/plans-for-week-and-presentations/</link>
      <pubDate>Mon, 28 Nov 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/plans-for-week-and-presentations/</guid>
      <description>I&amp;rsquo;ve posted the Schedule for Presentations and a Plan for this week on the github discussions site. (Everyone should get email notifications for these from the github site (if not, check that you have the &amp;ldquo;Watch&amp;rdquo; selected for the repository), but I&amp;rsquo;m posting redundantly here in case you are not getting them.)</description>
    </item>
    
    <item>
      <title>Class 21: Computational Epidemiology</title>
      <link>https://computingbiology.github.io/class21/</link>
      <pubDate>Mon, 21 Nov 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class21/</guid>
      <description>Class 21 was a guest leacture by Jack Heavey on Computational Epidemiology.
Here are the slides: Computational Epidemiology</description>
    </item>
    
    <item>
      <title>Class 20: Death and Cancer</title>
      <link>https://computingbiology.github.io/class20/</link>
      <pubDate>Thu, 10 Nov 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class20/</guid>
      <description>Slides and Links Slides: Class 20: Death and Cancer
  CDC WONDER Death Statistics
  Peyton Rous. A Sarcoma of the Fowl Transmissible by an Agent Separable from the Tumor Cells. Journal of Experimental Medicine. April 1911.
  Kimberly M. Newkirk, Erin M. Brannick, and Donna F. Kusewitt. Neoplasia and Tumor Biology (Chapter 6 from Pathologic Basis of Veterinary Disease). 2017.
  Robert J. Duronio and Yue Xiong.</description>
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    <item>
      <title>Class 22: Programmable Pharmaceuticals</title>
      <link>https://computingbiology.github.io/class22/</link>
      <pubDate>Thu, 10 Nov 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class22/</guid>
      <description>Slides and Links Slides: Class 22: Programmable Pharmaceuticals
  Michael Bretthauer, Magnus Løberg, Paulina Wieszczy, Mette Kalager, Louise Emilsson, Kjetil Garborg, Maciej Rupinski, Evelien Dekker, Manon Spaander, Marek Bugajski, Øyvind Holme, Ann G. Zauber, et al., for the NordICC Study Group. Effect of Colonoscopy Screening on Risks of Colorectal Cancer and Related Death. New England Journal of Medicine, October 2022.
  Zhen Xie, Liliana Wroblewska, Laura Prochazka, Ron Weiss, Yaakov Benenson.</description>
    </item>
    
    <item>
      <title>Class 19: Prime Editing</title>
      <link>https://computingbiology.github.io/class19/</link>
      <pubDate>Thu, 03 Nov 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class19/</guid>
      <description>Schedule Project Reports are due on Monday, 7 November (AoE).
Use this form to submit your project: Project Report Form
Tuesday, November 8 is Election Day (and a UVA class holiday — no class on Tuesday).
Quiz 2 Quiz 2 was today in class.
Slides and Links Slides: Class 19: Even Crispyr CRISPR
  Andrew V. Anzalone, Peyton B. Randolph, Jessie R. Davis, Alexander A. Sousa, Luke W. Koblan, Jonathan M.</description>
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    <item>
      <title>Class 18: Crispyr CRISPR</title>
      <link>https://computingbiology.github.io/class18/</link>
      <pubDate>Tue, 01 Nov 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class18/</guid>
      <description>Schedule (repeated from Class 16)
Quiz 2 will be on Thursday, November 3 and will focus on material from Classes 14 – 18 (mostly on editing genomes, but also including most likely one question on the discussion of Quiz 1 from Class 14.)
Project reports are due Monday, 7 November. This should be a complete project report, which will be graded. You will receive feedback on it, and have an opportunity to revise and improve.</description>
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    <item>
      <title>Class 17: CRISPR for Humans</title>
      <link>https://computingbiology.github.io/class17/</link>
      <pubDate>Thu, 27 Oct 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class17/</guid>
      <description>Schedule and Readings (repeated from Class 16)
Quiz 2 will be on Thursday, November 3 and will focus on material from Classes 14 – 18 (mostly on editing genomes, but also including most likely one question on the discussion of Quiz 1 from Class 14.)
Project reports are due Monday, 7 November. This should be a complete project report, which will be graded. You will receive feedback on it, and have an opportunity to revise and improve.</description>
    </item>
    
    <item>
      <title>Class 16: CRISPR in Bacteria</title>
      <link>https://computingbiology.github.io/class16/</link>
      <pubDate>Mon, 24 Oct 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class16/</guid>
      <description>Schedule Quiz 2 will be on Thursday, November 3 and will focus on material from Classes 14 – 18 (mostly on editing genomes, but also including most likely one question on the discussion of Quiz 1 from Class 14.)
Project reports are due Monday, 7 November. This should be a complete project report, which will be graded. You will receive feedback on it, and have an opportunity to revise and improve.</description>
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    <item>
      <title>Class 15: Recombinant DNA</title>
      <link>https://computingbiology.github.io/class15/</link>
      <pubDate>Thu, 20 Oct 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class15/</guid>
      <description>Schedule Quiz 2 was originally scheduled to be October 27, but since we won&amp;rsquo;t have finished genome editing until later, it is now rescheduled for November 3. (Quiz 3 will also be rescheduled for some later date.)
Project reports are due Monday, 7 November. This should be a complete project report, which will be graded. You will receive feedback on it, and have an opportunity to revise and improve.
Slides and Links The slides are here: Class 15: Recombinant DNA</description>
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    <item>
      <title>Class 14: Editing Genomes</title>
      <link>https://computingbiology.github.io/class14/</link>
      <pubDate>Tue, 18 Oct 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class14/</guid>
      <description>Slides The slides are here: Class 14: Editing Genomes
Some links to materials for the class:
  Wladyslaw Altermann, Józef Kazmierczak. Archean microfossils: a reappraisal of early life on Earth (Describes fossils of life from over 3.4 Billion years ago.)
  Carl R. Woese and George E. Fox. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proceedings of the National Academy of Sciences, November 1977. (As reported in New York Times: Scientists Discover a Form of Life That Predates Higher Organisms, 3 November 1977.</description>
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    <item>
      <title>Class 13: Genotypes and Phenotypes</title>
      <link>https://computingbiology.github.io/class13/</link>
      <pubDate>Tue, 11 Oct 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class13/</guid>
      <description>Final Project The Project Proposal is due Friday 14 October.
Use the Project Proposal Submission Form to submit your proposal, which should be a single PDF file containing answers to the seven questions below:
  The names and email ids for all members of your team.
  Title of your project: short description that clearly captures your project idea.
  A short paragraph that describes the goal of your project.</description>
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    <item>
      <title>Class 12: Computing with DNA</title>
      <link>https://computingbiology.github.io/class12/</link>
      <pubDate>Thu, 06 Oct 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class12/</guid>
      <description>Final Project Everyone in the class should have received email from me about your Project Team and Idea submission, and should be on track with your final project.
The next deliverable for the final project is the Project Proposal, due Friday 14 October. It should include:
  The names and email ids for all members of your team.
  Title of your project: short description that clearly captures your project idea.</description>
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    <item>
      <title>Class 11: Implementing DNA Storage</title>
      <link>https://computingbiology.github.io/class11/</link>
      <pubDate>Thu, 29 Sep 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class11/</guid>
      <description>Final Project The first deliverable for the Final Project is the Project Team and Idea Form, which we discussed in class today. It is due tomorrow, Friday, 30 September (AoE). See the Final Project Page for more information on the final project.
Reading Assignment October 3 – 4 are Fall &amp;ldquo;Reading Days&amp;rdquo;. I will be out of town and not have my usual office hours on October 3. Your reading assignment (to complete before our next class on Thursday, October 6) is this paper on computing with DNA:</description>
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    <item>
      <title>Class 10: DNA Storage</title>
      <link>https://computingbiology.github.io/class10/</link>
      <pubDate>Tue, 27 Sep 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class10/</guid>
      <description>Project 2 Project 2 is due tomorrow (Wednesday, 28 September) at 8:59pm.
Final Project The first deliverable for the Final Project is the Project Team and Idea Form, which we discussed in class today. It is due Friday, 30 September (AoE). See the Final Project Page for more information on the final project.
Slides The slides are here: Class 10: DNA Storage
Some links to materials for the class:
  Catherine Taylor Clelland, Viviana Risca, and Carter Bancroft.</description>
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    <item>
      <title>Final Project</title>
      <link>https://computingbiology.github.io/finalproject/</link>
      <pubDate>Mon, 26 Sep 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/finalproject/</guid>
      <description>Your final project can be on anything you want that is related to this course. We want your final projects to be interesting and fun to work on, and to produce something of value beyond just satisfying an expectation of this course.
We are open to other types of projects, but are expecting most students will do one of these types of projects:
  Systematization Projects: Start with a curious question, learn what is currently understood about it from the research literature, and produce something to explain it to computer scientists.</description>
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    <item>
      <title>Class 9: Distance-Based Phylogeny</title>
      <link>https://computingbiology.github.io/class9/</link>
      <pubDate>Thu, 22 Sep 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class9/</guid>
      <description>Project 2 Project 2 is now due Wednesday, 28 September, 8:59pm.
Final Project The first deliverable for the Final Project is due Friday, 30 September, 8:59pm. This is just a form submission to provide your team and idea for the final project, or other information if you need help to find a team or idea.
Slides The slides are here: Class 9: Distance-Based Phylogeny
Some links to materials for the class:</description>
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    <item>
      <title>Class 8: Phylogeny</title>
      <link>https://computingbiology.github.io/class8/</link>
      <pubDate>Thu, 15 Sep 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class8/</guid>
      <description>Project 2 The deadline for Project 2 has been extended to Monday, 26 September, 8:59pm.
Readings See Class 5 for this week&amp;rsquo;s readings.
Slides The slides are here: Class 8: Phylogeny
Some links to materials for the class:
  Georgia Ray (&amp;ldquo;Eukaryote Write Blog&amp;rdquo;), There’s no such thing as a tree (phylogenetically). May 2021.
  Thomas Bayes, conveyed by Mr. Price, As Essay towards solving a Problem in the Doctrine of Chances, 1763.</description>
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    <item>
      <title>Class 7: Estimating Evolutionary Distance</title>
      <link>https://computingbiology.github.io/class7/</link>
      <pubDate>Tue, 13 Sep 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class7/</guid>
      <description>Project 2 Project 2 is now posted, and is due on Wednesday, 21 September, 8:59pm.
Correction to Alignment Code! As was noticed in class today, the code for the gap-based alignment algorithms is wrong. The loops should include all values up to and including j (so should be
range(1, j + 1) instead of
range(1, j) (note that range in Python iterates through the values from the first input up to, but not including, the second input value, so to include j in the iteration, we need to use j + 1 in the range).</description>
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    <item>
      <title>Class 6: Alignment Algorithms</title>
      <link>https://computingbiology.github.io/class6/</link>
      <pubDate>Thu, 08 Sep 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class6/</guid>
      <description>Project 2 Project 2 is now posted, and is due on Wednesday, 21 September, 8:59pm.
Office Hours Update The location for Ashley&amp;rsquo;s office hours has moved to Olsson Hall 204. Other than the location, the office hours schedule is unchanged:
Monday, 11am-noon: Jack (Rice 414)
Monday, 1:30-2:45pm: Dave (Rice 507)
Wednesday, noon-1pm: Ashley (Olsson 204)
Wednesday, 2-3pm: Jack (Rice 414)
Friday, 11:30am-12:30pm: Ashley (Olsson 204)
Readings (Repeated from Class 5)</description>
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    <item>
      <title>Project 2: Sequence Alignment and Phylogeny</title>
      <link>https://computingbiology.github.io/project2/</link>
      <pubDate>Thu, 08 Sep 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/project2/</guid>
      <description>Due: Wednesday, 21 September, 8:59pm To get started on Project 2, one of the team members should fork this github repo: https://github.com/computingbiology/Project-2-2022F (just like you did for Project 1).
 jupyter notebook project2.ipynb
Follow the directions in that file for what to do, including how to submit the assignment using this form: https://forms.gle/gv144kv3KRo67uUX7
Happy Aligning!</description>
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      <title>Class 5: Analyzing Genomes</title>
      <link>https://computingbiology.github.io/class5/</link>
      <pubDate>Tue, 06 Sep 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class5/</guid>
      <description>Readings Before Thursday, 8 September:
 Read Chapter 5 of the Bioinformatics Algorithms: How do we compare biological sequences?.  Before next Tuesday, 13 September:
 Read Chapter 19 &amp;ndash; 27 of Hubert&amp;rsquo;s The DNA Book. (Chapter 20 is a bit different, but may be useful to give you ideas for the kinds of things you could do for the Final Project.)  Before next Thursday, 15 September:
 Chapter 26 of Manolis Kellis et al.</description>
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      <title>Class 4: The Human Genome</title>
      <link>https://computingbiology.github.io/class4/</link>
      <pubDate>Thu, 01 Sep 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class4/</guid>
      <description>Getting Email Notifications To get email notifications when there are posts in the Discussions site, you should select the &amp;ldquo;Watch&amp;rdquo; menu (upper right on https://github.com/computingbiology/fall2022) and select the notification you want. We recommend at least selecting from the &amp;ldquo;Custom&amp;rdquo; menu to get notifications for &amp;ldquo;Discussions&amp;rdquo; (if you want notifications for any updates, just select &amp;ldquo;All Activity&amp;rdquo;).
Schedule and Readings Project 1 is due on Monday, September 5 (8:59pm). See the project for submission instructions.</description>
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      <title>Class 3: Reading Genomes</title>
      <link>https://computingbiology.github.io/class3/</link>
      <pubDate>Tue, 30 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class3/</guid>
      <description>Schedule and Readings Before Monday, 31 January:
 Read Chapter 11 &amp;ndash; 18 of Hubert&amp;rsquo;s The DNA Book. Finish reading Chapter 3 (including 3.9) of the Bioinformatics Algorithms: How do we assemble genomes?.  Project 1 is due on Monday, September 5 (8:59pm). Everyone should have a partner for Project 1, and be making progess on it. If you don&amp;rsquo;t have a partner for it, let Prof. Evans know.
Slides The slides are here: Class 3: Reading Genomes</description>
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      <title>Office Hours</title>
      <link>https://computingbiology.github.io/officehours/</link>
      <pubDate>Tue, 30 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/officehours/</guid>
      <description>The office hours schedule has been updated:
Monday, 11am-noon: Jack (Rice 414)
Monday, 1:30-2:45pm: Dave (Rice 507)
Wednesday, noon-1pm: Ashley (Olsson 204)
Wednesday, 2-3pm: Jack (Rice 414)
Friday, 11:30am-12:30pm: Ashley (Olsson 204)
To schedule other times to meet with Dave use: https://davidevans.youcanbook.me/.</description>
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      <title>Class 2: The Platform for Life on Earth</title>
      <link>https://computingbiology.github.io/class2/</link>
      <pubDate>Thu, 25 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class2/</guid>
      <description>Project 1 Project 1 is now posted, and is due on Monday, September 5 (8:59pm). Students will work in teams of two for Project 1, with constraints as discussed in Class 2: you can choose your partner or be assigned one “randomly” after class (today). If you choose your own partner, your team must satisfy these constraints:
 Both teammates went to different high schools Your answers to at least one of these questions must be different:  What country were you born in?</description>
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      <title>Project 1: Assembling Genomes</title>
      <link>https://computingbiology.github.io/project1/</link>
      <pubDate>Thu, 25 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/project1/</guid>
      <description>Due: Monday, 5 September, 8:59pm If you don&amp;rsquo;t have Jupyter installed, you&amp;rsquo;ll need to install this first:
 pip install jupyterlab
or see https://jupyter.org/install for more details and other options.
Then, to get started on Project 1, one of the team members should fork this github repo: https://github.com/computingbiology/Project-1-2022F (you can do this by clicking the &amp;ldquo;Fork&amp;rdquo; button at the top right of the page)
Clone your forked repository to have a local copy to work on:</description>
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    <item>
      <title>Class 1: Life</title>
      <link>https://computingbiology.github.io/class1/</link>
      <pubDate>Tue, 23 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/class1/</guid>
      <description>Schedule and Readings Before 8:59pm Wednesday 24 August:
 Read the Syllabus, Pledge, and complete the Registration Survey. After you submit the Registration Survey, you will receive an invitation (to the github account you include in your survey) to join the course github site (which will enable you to join the github discussions).  Before Tuesday&amp;rsquo;s class, 30 August:
  Read Chapters 1 &amp;ndash; 10 of Hubert&amp;rsquo;s The DNA Book (the chapters are very short and interesting, so its not as much as it sounds).</description>
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      <title>Computer Science Background</title>
      <link>https://computingbiology.github.io/computer-science-background/</link>
      <pubDate>Mon, 22 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/computer-science-background/</guid>
      <description>Here is a guide to the computing theory background expected for students entering this course.
If you&amp;rsquo;ve completed cs 2130 (Computer Systems and Organization 1) and a good Theory of Computation or Algorithms course (the official pre-requisites for this course) and remember the big ideas from that class, this should all be familiar to you already, but it may still be useful to refresh your understanding using these materials.
If you haven&amp;rsquo;t taken the prerequisite courses and are getting up to speed on your own, we hope these materials will be helpful.</description>
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      <title>Cost of Computation</title>
      <link>https://computingbiology.github.io/complexity/</link>
      <pubDate>Mon, 22 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/complexity/</guid>
      <description>When we consider the power of our computing models, we have been concerned with understanding what functions can be computed (in theory, which means without any arbitrary limits on their execution) by different computing models. When we want to actual compute using physical computers, cost matters.
For concerete computations where we already know the input and have an implementation of the algorithm, we can measure the cost of executing the algorithm by just running it and recording the cost.</description>
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    <item>
      <title>Course Pledge</title>
      <link>https://computingbiology.github.io/pledge/</link>
      <pubDate>Mon, 22 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/pledge/</guid>
      <description>Honor Expectations As a student at the University of Virginia, you are trusted to be honorable and expected to behave in ways that merit that trust. We take advantage of this trust to provide a better learning environment for everyone. In particular, students in this course are expected to follow these rules throughout the course:
I will not lie, cheat or steal. If I am unsure whether something would be considered lying, cheating or stealing, I will ask before doing it.</description>
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    <item>
      <title>Models of Computation</title>
      <link>https://computingbiology.github.io/models/</link>
      <pubDate>Mon, 22 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/models/</guid>
      <description>To reason precisely about what computers can and cannot do, we need abstract models that capture the things we think are important but avoid the complexities of physical objects.
Models and Mathematics The physical world is messy and suffers from arbitrary limits — this applies both to the physical computing devices we use (which always have some probability of failing and can&amp;rsquo;t even do arithmetic correcly) and even more so to biological systems we consider in this class.</description>
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    <item>
      <title>Registration Survey</title>
      <link>https://computingbiology.github.io/registration-survey/</link>
      <pubDate>Mon, 22 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/registration-survey/</guid>
      <description>Everyone in the class should submit this course registration survey by Wednesday, 24 August at 7:59pm.</description>
    </item>
    
    <item>
      <title>Schedule</title>
      <link>https://computingbiology.github.io/schedule/</link>
      <pubDate>Mon, 22 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/schedule/</guid>
      <description>Weekly Schedule Class Meetings
Tuesdays and Thursdays, 12:30pm – 1:45pm in Olsson Hall 120.
Office Hours
(29 August – 6 December)
Monday, 11am-noon: Jack (Rice 414)
Monday, 1:30-2:45pm: Dave (Rice 507)
Wednesday, noon-1pm: Ashley (Olsson 204) Wednesday, 2-3pm: Jack (Rice 414)
Friday, 11:30am-12:30pm: Ashley (Olsson 204)
To schedule other times to meet with Dave use: https://davidevans.youcanbook.me/.
Semester Schedule 23 August: Class 1: Life
 What is Life? Plan for the Course Carbon-Based Life  25 August: Class 2: Platform for Life on Earth</description>
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    <item>
      <title>Syllabus</title>
      <link>https://computingbiology.github.io/syllabus/</link>
      <pubDate>Mon, 22 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/syllabus/</guid>
      <description>This syllabus is a &amp;ldquo;semi-living document&amp;rdquo; (i.e., more like a virus than a bacterium) subject to change as we adapt during the semester. The course website is managed through a public github repository, so you can see past versions and changes there.
The version as posted on the first day of class is available here, and history of changes.

Overview Course Description: This course will look at connections between computing and biology, with a focus on DNA.</description>
    </item>
    
    <item>
      <title>Syllabus Posted</title>
      <link>https://computingbiology.github.io/syllabus-posted/</link>
      <pubDate>Mon, 22 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/syllabus-posted/</guid>
      <description>The course syllabus is now posted (but may be slightly revised before the course starts).</description>
    </item>
    
    <item>
      <title>Fall 2022 Course</title>
      <link>https://computingbiology.github.io/fall2022/</link>
      <pubDate>Sun, 21 Aug 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/fall2022/</guid>
      <description>Welcome to the cs4501: Computational Biology / Biological Computing Fall 2022 course site.
The Fall 2022 course is scheduled for Tuesdays and Thursdays, 12:30-1:45pm in Olsson Hall 120.
The course will be similar to the Spring 2022 course (which you can explore here, including the Syllabus and Schedule. Versions of these for the Fall 2022 course will be posted here soon.</description>
    </item>
    
    <item>
      <title>Course Registration Survey</title>
      <link>https://computingbiology.github.io/survey/</link>
      <pubDate>Mon, 17 Jan 2022 00:00:00 +0000</pubDate>
      <author>evans@virginia.edu (David Evans)</author>
      <guid>https://computingbiology.github.io/survey/</guid>
      <description>Please submit this survey if you are enrolled in the class or wanting to join the class:
 https://forms.gle/8KucndY5iYcPPLcu6   Before completing the survey, you should read the Syllabus and Course Pledge.</description>
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