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Spring School in the Systems Biology of Neurodegenerative Disease

Offered for academic credit as BCH8110: Advanced Topics in Systems Biology (3 cr.) Course Coordinator: Dr Steffany Bennett Participating Faculty: Dr Stephen Fai Email: sbennet@uottawa.ca Limited enrolment Dates: May 19- May 29th 2015 Class Website: https://www.med.uottawa.ca/lipidomics/courses_summer2015.html Description: Each academic year, our faculty offers a Spring, Summer, Fall, or Winter School in Systems Biology organized by the CIHR Training Program in Neurodegenerative Lipidomics and the Ottawa Institute of Systems Biology. The School can be taken for academic credit through the University of Ottawa as BCH8110 Advanced Topics in Systems Biology.

The school offers a unique two-week intensive training in systems biology with focus on training scientists to overcome some of the challenges facing our understanding and treatment of intractable neurodegenerative disease.

The 2015 Spring School consists of:

• formal lectures discussing the “omics” of neurodegenerative disease,

• hands-on training familiarizing students with recent methodological advances and analytical techniques in two “omics” aspects: (1) lipidomics and (2) 3D brain information modelling as they are applied to neurodegenerative disease,

• dry-bench “omic” laboratories where students complete a defined project addressing a question specific to each student using data generated in collaboration,

• Groups of three trainees will be assigned to one of three labs (two in neurolipidomics, and one in brain information modelling). In each lab, demonstrators (Katie Graham, Matthew Granger, and Samantha Sherman) led by one professor Dr. Steffany Bennett or Dr. Stephen Fai will provide one-on-one training with the technologies and softwares required to (a) generate and analyze lipidomic data (neurolipidomics laboratories) or (b) build a brain information model to be used the management of lipidomic data. At the end of the course, students in the three labs will come together and present their projects to the entire group. A final assignment will be completed after the laboratory sessions wherein students in the neurolipidomics laboratories combine all of their datasets and write mock “results” and “discussion” section of a PlosOne paper. Students in the brain information modelling laboratory will write a short review paper, describing the use and bioinformatic set-up of existing brain information models and how these models as well as the information systems used in building information models can be applied to their brain information model to generate a repository for lipidomic

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datasets.

Participants: The Spring School is open to medical students, graduate students, post-doctoral fellows, research associates, professors, industrial professionals, and government researchers from the information sciences (e.g., systems engineering, information technology) and the life sciences (e.g., neuroscience, biochemistry, physiology, biology, systems biology) interested in developing their skills in systems biology, information modeling, visualization, and metabolic approaches to studying neurodegenerative disease. Preference will be given to graduate students currently enrolled in a related program of study and fellows currently employed in related fields including neuroscience, systems biology, cell biology, biochemistry, structural biology, behavioural psychology, biostatistics, neurology, nanotechnology, systems engineering, computer science, and information sciences.

Fees: The summer school course can also be taken for official University of Ottawa credit (3 credits) by paying additionally the tuition fees corresponding to your situation (Canadian or foreign fees). This can be determined from the webpage http://www.registrar.uottawa.ca/Default.aspx?tabid=4168. There is no tuition for academic participants (graduate students, PDFs, professors) not requesting credit. There is a $2000 fee for non-academic participants.

Prerequisites: For students/PDFs in the information sciences: Proof of registration in an accredited degree program or post-doctoral position and proof of 4th year or graduate level courses in digital modeling, 3D imaging, or information modeling, visualization, or simulation (information sciences) will be required to confirm registration. For students in the life/basic sciences: Proof of registration in an accredited degree program or post-doctoral position and proof of 4th year or graduate level courses in life/basic sciences. For non-academic participants: Proof of academic or significant work-experience in digital modeling, 3D imaging, information modeling, visualization, simulation, life sciences, or molecular biology. Registration will be open to highly qualified personnel subject to approval of the course coordinators.

Evaluation: Attendance at all lectures, laboratories, oral presentation of research results, and written report of research results is mandatory for both auditors and students taking the course for credit. The mark will be based on evaluation of a laboratory project. Projects will be marked by the school faculty (professors and demonstrators). Students not taking the course for credit will receive a letter stating that they satisfactorily participated in the Spring school. Those enrolled for credit will receive their mark from the Office of the Registrar (University of Ottawa) at the end of the university term. Final grade is based on the following:

• Class participation: 10% (any missed class or laboratory will result in the grade of 0 for both components and loss of the confirmatory certificate/letter of participation)

• Laboratory participation: 20% (any missed class or laboratory will result in the grade of 0 for both components and loss of the confirmatory certificate/letter of participation)

• Accomplishment and accuracy of laboratory-specific milestones: 55% • Written report: 15% (Each student registered for credit will submit an individual report.) Due:

June 19 2015 (emailed to Dr. Steffany Bennett by midnight (sbennet@uottawa.ca). Late submissions will receive a 5% deduction per day).

Policy on Academic Fraud: Plagiarism or academic fraud will not be tolerated. Plagiarism will be discussed explicitly in the first class. This class conforms entirely to the University of Ottawa’s Academic Regulation 14. The definition and sanctions provided below are cited directly from http://www.uottawa.ca/about/academic-regulation-14-other-important-information. Italics indicate this direct citation.

Preamble Academic integrity is a fundamental value at the core of all academic activities. The regulation on academic fraud defines the acts that can compromise academic integrity, and outlines the consequences of such acts and the formal disciplinary procedures in place. Further information on academic integrity is available in the University of Ottawa’s Academic Integrity Student Guide.

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Beyond educational measures that professors may take, the University of Ottawa has two processes in place for handling cases of academic fraud —the regular process and the accelerated process. The University is committed to upholding the integrity of the process for handling academic fraud (PDF). Disclosure of the identity of any student accused of academic fraud or the person(s) alleging academic fraud is limited by the Freedom of Information and Protection of Privacy Act (FIPPA). Only the results of the investigation can be disclosed to the person who submitted an allegation of academic fraud. Definition 1. Any act by a student that may result in a distorted academic evaluation for that student or another student. Academic fraud includes but is not limited to activities such as:

a) plagiarising or cheating in any way; b) submitting work not partially or fully the student’s own, excluding properly cited quotations and references. Such work includes assignments, essays, tests, exams, research reports and theses, regardless of whether the work is in written, oral or another form; c) presenting research data that are forged, falsified or fabricated. d) attributing a statement of fact or reference to a fabricated source; e) submitting the same work or a large part of the same piece of work in more than one course, or a thesis or any other piece of work submitted elsewhere without the prior approval of the appropriate professors or academic units; f) falsifying or misrepresenting an academic evaluation, using a forged or altered supporting document or facilitating the use of such a document; g) taking any action aimed at falsifying an academic evaluation.

Sanctions Note: For cases involving graduate courses, the following sanctions are imposed by the Faculty of Graduate and Postdoctoral Studies (FGPS). 2. Students who commit or attempt to commit academic fraud, or who are a party to academic fraud, are subject to one or more of the sanctions below. All sanctions are effective immediately, notwithstanding an appeal. If a student withdraws from a course following an allegation of fraud filed against the student, the University may re-register the student in the course in question. Sanctions stipulated in sections 2(a) to 2(f) inclusively, are imposed by the faculty offering the course. Sanctions should be accompanied by a follow-up mechanism, such as mandatory meetings with appropriate persons or services, e.g. the mentoring centre, the Academic Writing Help Centre (AWHC), etc.

a) a written warning; b) zero for part of the work in question; c) zero for the work in question; d) zero for the work in question and the loss of additional marks for the course in question; e) zero for the work in question, with a final grade no higher than the passing grade for the course in question; f) an F grade for the course in question. Sanctions stipulated in sections 2(g) to 2(i) inclusively are imposed by the faculty offering the course, after consulting with the student’s home faculty. g) the addition of another 3 to 30 credits to the student’s program requirements or to the requirements of any program at the same level in which the student subsequently registers. h) suspension of a University of Ottawa or faculty scholarship for a specified period; i) the loss of any faculty or University scholarship opportunity; Sanctions stipulated in sections 2(j) to 2(n) inclusively are imposed by the Senate Appeals Committee upon recommendation of the student’s home faculty. The decision of the Senate Appeals Committee takes effect immediately.

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j) suspension from the University for a maximum of two years. No course taken at the University of Ottawa or elsewhere during the suspension period will be recognized by the University and no tuition fees will be refunded. Once the suspension ends, the student can re-register in the program and is subject to the program requirements in place at that time. k) inclusion of a permanent statement on the student’s official transcript: Sanction pursuant to contravention of the University regulation on fraud. l) expulsion from the University of Ottawa and permanent statement on the student’s official transcript indicating the student was expelled from the University for committing academic fraud. Three years following the date of expulsion, the student is eligible to make a request to the Senate Appeals Committee to have the expulsion set aside, including the possibility, where applicable, of having the mention removed from the student’s transcript. If the student reapplies to the University of Ottawa, the regular admission process applies. m) cancellation or revocation of a degree, diploma or certificate conferred prior to the University becoming aware of academic fraud; n) any other sanction considered appropriate for the circumstances.

Deadlines: Registration: April 1 2015: To pre-register and apply for accommodation/travel funding (with or without academic credit) April 22 2015: To register for academic credit as BCH8110 May 1 2015: To register without late fees School Dates: May 19- May 29 2015 (10:00-4:00): School dates (Milestones hand-in dates indicated in schedule) May 29 2015: Formal presentation of results June 19 2015: Written report due (for those registered for academic credit in BCH8110). Funding: In 2015, this course receives funding from the STIHR/CIHR Training Program in Neurodegenerative Lipidomics (TGF-96121) and the Faculty of Medicine Biochemistry Graduate Program. These funds support the travel expenses of the invited speakers, laboratory reagents required for the course, provide financial support for travel and accommodation for students and post-docs registered at Canadian universities attending the Spring School and Outreach Program, and demonstrator teaching assistantships.

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DEADLINES This school is designed to enable trainees to work on real datasets and provide these highly qualified personnel with the necessary professional training and practical employer-ready skills to meet the needs of both academic placements (PDF and faculty positons) and pharma industries (i.e., introduction of milestones). Milestone deadlines: Lipidomics Labs:

• Wed May 20 4:00 Milestone 1 due: Quiz hand-in rm 4260 RGN to Matthew Granger and Samantha Sherman

• Mon May 25 10:00 Milestone 2 due: Acquisition dataset hand-in rm 4260 RGN to Matthew Granger and Samantha Sherman

• Tues May 26 10:00 Milestone 3a (Lipidomic group) due: Alignment dataset hand-in On Dropbox or by WeTransfer

• Tues May 26 4:00 Milestone 3b (Lipidomic group) due: Alignment dataset hand-in On Dropbox or by WeTransfer

• Thurs May 28 10:00 Milestone 4 (Lipidomics group) due: Normalization dataset hand-in On Dropbox or by WeTransfer

• Friday May 29 4:00 Milestone 5 due: Statistic dataset hand-in On Dropbox or by WeTransfer

Brain Information Modelling Lab:

• Wed May 20 4:00 Milestone 1 due: Quiz hand-in rm 4260 RGN to Dr Bennett

• Mon May 25 10:00 Milestone 2 due: Planes dataset hand-in On Dropbox or by WeTransfer

• Thurs May 28 4:00 Milestone 3 due: Anatomical volume dataset hand-in On Dropbox or by WeTransfer

• Fri May 29 2:00 Milestone 4 due: Integration of all anatomical volumes into one model On Dropbox or by WeTransfer

Project deadlines:

• Fri June 26: Before Midnight by email to Dr Bennett Written report due

Written Report Lipidomics: Students will combine all of their datasets and write mock “results” and “discussion” section of a PlosOne paper.

Written Report Brain information modelling: Students will write a short review paper, describing the use and bioinformatic set-up of existing brain information models and how these models as well as the information systems used in building information models can be applied to their brain information model to generate a repository for lipidomic datasets.

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Directions to CIMS lab: Carleton Immersive Media Studio Carleton University Visualization and Simulation Building, Fourth Floor 1125 (is ground floor when entering main entrance from Parking Lot#1) Colonel By Drive Ottawa, ON, K1S5B6 To enter security door: Call X4204 at security telephone (ask for your teaching assistant Katie Graham to be buzzed in)

Higher resolution image: http://carleton.ca/campus/map/ (Select the Visualization and Simulation Building)