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Natural Computing The University of Western Ontario Computer Science 9835b, Winter 2016-17 NATURAL COMPUTING Description Natural computing is the field of research that investigates models and com- putational techniques inspired by nature and, dually, attempts to understand the world around us in terms of information processing. It is a highly interdis- ciplinary field that connects the natural sciences with computing science, both at the level of information technology and at the level of fundamental research. Natural Computing comprises three main branches: human-designed com- putation inspired by nature, novel natural implementation substrates, and the computational aspects of processes taking place in nature. Natural phenom- ena that inspired computation paradigms include self-reproduction (cellular au- tomata), the functioning of the brain (neural computation) Darwinian evolution (evolutionary computation), group behaviour (ant algorithms), the immune sys- tems (artificial immune systems), the characteristics of life (artificial life), cell membranes (membrane computing), and morphogenesis (amorphous comput- ing). These paradigms can be implemented either on traditional hardware or on alternative physical media such as biomolecular (DNA, RNA) computing or trapped-ion quantum computing devices. Dually, natural processes that can be viewed as information processing abund, and include gene regulatory net- works, protein-protein interaction networks, biological transport networks and gene-assembly in unicellular organisms. In the same vein, efforts to understand biological systems include engineering semi-synthetic organisms and attemtping to understand the universe in terms of information processing. This course presents an overview of natural computing, with an emphasis on biomolecular (DNA) computing, cellular computing and quantum computing. Course webpage: http://www.csd.uwo.ca/~lila/naco16-17.html Prerequisites The course has no formal prerequisites. However, students with backgrounds other than computer science should contact the instructor. Instructor Lila Kari 385 Middlesex College Tel. 661 2111 ext. 86894 [email protected] http://www.csd.uwo.ca/~ lila, 1 Class meetings Tuesdays, 10:30am-12:30pm, Thu. 12:30pm-1:30pm, room MC320. Office hours Wednesdays, 1:30pm-3:30pm, MC 385. Topics • Introduction to Natural Computing • Encoding information in DNA • Bio-operations • DNA models of computation • Cellular computing • DNA nanocomputation by self-assembly • Quantum computing • Other areas of natural computing Student evaluation Each student will give a lecture on a topic agreed on with the instructor and submit a term paper on the same topic. The marks will be calculated as 50% for the paper, 40% for the presentation and 10% for class participation. Student presentations start after the Conference Week (Feb 20- Feb 23) and the exact date will depend on the class size and chosen topic. Final Paper due date: Wednesday, April 5, 2017 Email Contact You may contact the course instructor via e-mail with brief questions regard- ing course material or clarification of assignments. However, please first check the course website for answers to frequently asked questions, or to see if the information is already there, before e-mailing the instructor. You must include "CS9835" in the subject line (otherwise it might get filtered as spam). Please send E-mail from your UWO account and send E-mail in plain text format. We will occasionally need to send email messages to the whole class, or to students individually. Email will be sent to the UWO email address assigned to students by Information Technology Services (ITS), i.e. your email address @uwo.ca. It is each student's responsibility to read this email on a frequent and regular basis, or to have it forwarded to an alternative email address if preferred. See the ITS website for directions on forwarding email. You should note that email at ITS (your UWO account) and other email providers such as hotmail.com or yahoo.com may have quotas or limits on the 2 amount of space they can use. If you let your email accumulate there, your mailbox may fill up and you may lose important email from your instructors. Losing email that you have forwarded to an alternative email address is not an excuse for not knowing about the information that was sent. Support Services The Web sites for Registrarial Services http://www.registrar.uwo.ca, the Stu- dent Support Services provided by the USC listed here http://westernusc.ca/services and the Student Development Services http://www.sdc.uwo.ca are provided for easy access. Students who are in emotional/mental distress should refer to Mental Health@Western http://www.uwo.ca/uwocom/mentalhealth for a complete list of options about how to obtain help. Academic Accommodation for Medical Illness If you are unable to meet a course requirement due to illness or other serious cir- cumstances, you must provide valid medical or other supporting documentation to your Dean's office as soon as possible and contact your instructor immedi- ately. It is the student's responsibility to make alternative arrangements with their instructor once the accommodation has been approved and the instructor has been informed. In the event of a missed final exam, a "Recommendation of Special Examination" form must be obtained from the Dean's Office immedi- ately. For further information please see: http://www.uwo.ca/univsec/handbook/appeals/medical.pdf. A student requiring academic accommodation due to illness should use the Student Medical Certificate when visiting an off-campus medical facility or re- quest a Record's Release Form (located in the Dean's Office) for visits to Student Health Services. The form can be found here: https://studentservices.uwo.ca/secure/medical document.pdf. Accessibility Statement Please contact the course instructor if you require material in an alternate for- mat or if you require any other arrangements to make this course more accessible to you. You may also wish to contact Services for Students with Disabilities (SSD) at 661-2111 x 82147 for any specific question regarding an accommoda- tion. 3 Ethical Conduct Scholastic offences are taken seriously and students are directed to read the appropriate policy, specifically, the definition of what constitutes a Scholastic Offence, at the following Web site: http://www.uwo.ca/univsec/handbook/appeals/scholoff.pdf Plagiarism Students must write their essays and assignments in their own words. Whenever students take an idea, or a passage from another author, they must acknowledge their debt both by using quotation marks where appropriate and by proper ref- erencing such as footnotes or citations. Plagiarism is a major academic offence. The University of Western Ontario uses software for plagiarism checking. Students may be required to submit their written work and programs in elec- tronic form for plagiarism checking. All required papers may be subject to submission for textual similarity re- view to the commercial plagiarism detection software under license to the Uni- versity for detection of plagiarism. All papers submitted for such checking will be included as source documents in the reference database for the purpose of detecting plagiarism of papers subsequently submitted to the system. Use of the service is subject to the licensing agreement, currently between The University of Western Ontario and Turnitin.com (http://www.turnitin.com/). 4.
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