95631 CSC 181A - 0 Advanced Research Topics in Computer Science The Computer Science Lyceum (continued) Fall 2002 Friday 3 pm - 5:40 pm , Kramer Science Center 102A Herbert J. Bernstein (yaya@dowling.edu) Assignments

This web page is http://www.bernstein-plus-sons.com/.dowling/CSC181/CSC181_Assignments.html
Copyright © 2002 Herbert J. Bernstein. All rights reserved.

• Assignment #1, due 13 Sep 2002
  • Obtain the text books
  • Obtain a lab notebook with carbons
  • Do research and discover a connection among Voronoi (or Vornoi) diagrams, Delaunay diagrams and molecular surfaces
  • Be prepared next time to discuss your own proposed research topic(s) with the class

• Assignment #2, due 20 Sep 2002
  • Read Valiela, pp 1-48, and be prepared to discuss.
  • Download the PDB dataset 4ins from www.rcsb.org.
  • Write a program which extracts all the Carbon-Alpha atoms and lists them with their x, y and z coordinates. Test it on 4ins.
  • Find code to compute the Voronoi diagram of the Carbon-Alpha atoms of 4ins, run it and be prepared to discuss it.

• Assignment #3, due 27 Sep 2002
  • Read Tufte, pp 1-51, and be prepared to discuss.
  • In class on 20 Sep 2002, we will have discussed several alternatives for computation of the Voronoi diagram in 3 dimensions. You will each have been given one of those alternatives to find or code yourself. Take subsets of the 4ins Carbon-alpha data and run time trials on the method you are using sufficient to given an experimental indication of the rate of increase in computation time with the number of points. Try to provide a well-grounded theoretical estimate of the shape of this curve.

• Assignment #4, due 4 Oct 2002
  • Read Valiela, pp 49-77, and be prepared to discuss.
  • If you have not done any part of the prior reading, be sure to catch up on it now.
  • Start searching for algorithms to compute molecular surfaces.
  • In class on 27 Sep 2002, we will have looked at the preliminary results of your experiments with alternative algorithms for the computation of Voronoi diagrams in 3 dimensions. Now it is time to plan a serious, theoretically well-grounded, statistically valid search for a best way to design and implement the calculation of molecular surfaces. You may (should) consult with your colleagues in the class, but each of you must be prepared to present and discuss a plan of action.
  • Be prepared to turn in your notebook carbons
  • Start your own project web page with all references you have found so far. Find at least one journal article related to the calculation of 3-D Voronoi diagrams and/or molecular surfaces in a library, photocopy it and bring it to class, unstapled, so that we can make copies for all of us to share. Each person must bring a different journal article. It is fine to go to the library together, but each person must go, and each person must locate and copy at least one article. You may (should) use a computerized search to locate articles.

• Assignment #5, due 11 Oct 2002
  • Read Tufte, pp 52-87. Be prepared to discuss, but more importantly, apply to the statistical data on timing you have collected so far and to all further statistical data you collect and present.
  • Last time you started searching for molecular surface algorithms. Now select one such algorithm, find (or write) an implementation, and repeat your timing experiments with subsets of the 4ins Carbon-alpha data. Do collaborate with your classmates, but each person should be prepared to report on a different molecular surface algorithm.
  • Update own project web page with your statistical results and all new references you have found.

• Assignment #6, due 18 Oct 2002
  • Read Tufte, pp 90-105. Be prepared to discuss, but more importantly, review your graphics and try to increase the data-ink ratio.
  • Last time you started timing molecular surface algorithms. Now it is time to get together with your classmates and find a way to make your results comparable to one another's.
  • Update own project web page with your statistical results and all new references you have found.
  • Get together with your classmates and start a common course project web page on arcib.dowling.edu in the CSC181F02 account.

• Assignment #7, due 25 Oct 2002
  • Read Valiela, pp 183-217 (we'll come back to the chapters we skipped, but this aligns with what you just read in Tufte). Be prepared to discuss. In particular, using what you have read in Tufte and Valiela, add a discussion to your project web page about the various choices in how to present performance data about molecular surface algorithms and be prepared to propose a common approach to be put onto the project web page.
  • In collaboration with your classmates, start bringing your statistical results into a common set of inter-comparable charts with the same axes, and add them to the project web page. Make certain that you preserve the primary data and the adjusted data used to make the charts, so that when the discussion on how to present is settled, the charts can be redone to the agreed style. Make the primary data and the adjusted data behind each chart available via a link.
  • Where appropriate, replace links on the project web page which now point to your own web pages with the primary information and move all links to external web pages down to a properly annotated references section.

• Assignment #8, due 1 Nov 2002
  • Midterm warnings will be filed for this course on Wednesday, 30 October 2002. If you have not caught up on all past readings, your web page, and your contributions to the course web page by 5 pm on Tuesday, 29 October 2002, you must withdraw from this course or formal midterm warning will be filed.
  • During the lecture on 25 Oct 2002, each student remaining in the course did an informal presentation of their understanding of the state of the project, and of their contributions to it. Those who do not have the time or the interest to contribute fully to the course project will have been asked to withdraw. Those who remain will be expected to stay current on all course activities. To help ensure full participation, for each remaining meeting of the course, we will begin with a formal 10 minute presentation by each student of the same material. The source materials that may be used for each presentation are:
    • The course web page
    • The student's own web page
    • Written materials such as course carbons and papers from the literature, copies of which are provided on paper to all other students and the instructor.
    • Web links, .pdf's, .doc's, .ppts which have not been printed may not in general be used, but if printed copies have been provided at that meeting, they may be used.
  • Read Valiela, pp 78-125. Prepare a 2-page critique of the project, the project web page and of your own web page based on what you read in Valiela, submit it, and be prepared to discuss it after the formal presentation.
  • In collaboration with your classmates, start or continue bringing your statistical results into a common set of inter-comparable charts with the same axes, and add them to the project web page. Make certain that you preserve the primary data and the adjusted data used to make the charts, so that when the discussion on how to present is settled, the charts can be redone to the agreed style. Make the primary data and the adjusted data behind each chart available via a link.
  • Continue, where appropriate, replacing links on the project web page which now point to your own web pages or other web page with the primary information and move all links to external web pages down to a properly annotated references section.

• Assignment #9, due 8 Nov 2002
  • This meeting is the decision point as to which students (if any) will be asked to come to a meeting in the Spring. (An abstract is due in on the 15th). The basis on which the decision will be made is not which student has the best results, but which student(s) best present an overall understanding of the entire project. Make your 10 minute presentation for this class meeting as clean and coherent as possible, with slides done as bullets, one slide per html page. Be certain to have a slide with properly done references (pay careful attention to what is said and done in the lecture on 1 Nov). Be certain to give proper credit to your classmates.

• Assignment #10, due 15 Nov 2002
  • Counting the meeting on the 15th, there are three meetings of this class left, plus one meeting during finals week that will be used for presentations of work done. The meeting on the 15th will be the decision point for all material to be included in the joint project report, and the last two meetings will be devoted to bringing that material together. It is essential that the timings from different algorithms be brought into an intercomparable form before the meeting on the 15th. To that end, everyone should have run the algorithm(s) they are looking at on a significantly overlapping set of datasets before the meeting on the 15th and should have a chart of their timing ready.
  • It is essential that the Bibliography be completed before the meeting on the 15th.
  • Read Valiela, pp 127-169 (the chapters of writing a scientific paper and on other means of scientific communication). Using what you learn in these two chapters, revise your web page and/or add to your web page a clear short written scientific explanation of the work being presented on your web page, and integrate that material into the common course web page. Be certain to integrate text with figures and with references. Note that there will be no opportunities to make up this effort later in the course. We have other matters to deal with then.

• Assignment #11, due 22 Nov 2002
  • Finish reading both Valiela and Tufte. What they have to say will be useful to you in the rest of what we do.
  • in the meeting of 15 Nov 2002, we will have put together an abstract of the research. Now it is time to start putting together a full paper describing the research and the results. We cannot do that work in the short time left for class sessions, so it is critically important that each person do the tasks the will be assigned in the meeting of 15 Nov 2002 before the meeting of 22 November 2002. All major materials assigned must be ready as web documents or word documents from which copy and paste operations can be used to insert them into the draft paper. To prevent interruptions of a very demanding process, the door will be closed at 3 pm and nobody will be admitted late. Anyone who is not prepared or who does not participate in the joint activity will be asked to leave and will not be readmited. The work for this session cannot be made up at a later date. DO NOT BE LATE. We expect there to be some holes in what is produced at this class meeting. Assignments to fill those holes will be made at the class session of 22 November 2002, and a complete draft of the final paper will be put together under the same rules at the meeting of 6 December 2002. Those assignments will not be posted on this web page. The only way to get those assignments and to finish the course is to be a full participant on the 22nd.