Jozica Dolenc: Catalogue data in Autumn Semester 2021 |
| Name | Dr. Jozica Dolenc |
| Address | Inf.zentrum Chemie Biologie Phar. ETH Zürich, HCI J 57.4 Vladimir-Prelog-Weg 1-5/10 8093 Zürich SWITZERLAND |
| Telephone | +41 44 632 29 48 |
| dolenc@chem.ethz.ch | |
| Department | Chemistry and Applied Biosciences |
| Relationship | Lecturer |
| Number | Title | ECTS | Hours | Lecturers | |||||||||||||||||||||||||||||||||||||||||
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| 511-0007-00L | Scientific Writing and Presenting  Only for Pharmaceutical Sciences MSc. | 2 credits | 2G | J. A. Hiss, A. Burden, J. Dolenc, J.‑C. Leroux, O. Renn, C. Steuer | |||||||||||||||||||||||||||||||||||||||||
| Abstract | This introductory class provides an overview of the basic scientific writing techniques and a guideline to presenting scientific data, together with guided exercises and hands-on training. It is devised to accompany the research projects within the curriculum of the MSc in Pharmaceutical Sciences. | ||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The class enables the participants to prepare their own scientific texts and oral presentations, and critically assess the quality of the presentation of scientific data. | ||||||||||||||||||||||||||||||||||||||||||||
| Content | The participants receive an introduction to basic formal aspects of scientific writing and the design of graphical elements. Lectures and topical seminars alternate with practical task for the participants, which will be evaluated in a peer-to-peer setting. Performance feedback is provided by both the teachers and the peers. | ||||||||||||||||||||||||||||||||||||||||||||
| 529-0004-01L | Classical Simulation of (Bio)Molecular Systems  | 6 credits | 4G | P. H. Hünenberger, J. Dolenc, S. Riniker | |||||||||||||||||||||||||||||||||||||||||
| Abstract | Molecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS). | ||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Introduction to classical (atomistic) computer simulation of (bio)molecular systems, development of skills to carry out and interpret these simulations. | ||||||||||||||||||||||||||||||||||||||||||||
| Content | Molecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS). | ||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | The powerpoint slides of the lectures will be made available weekly on the website in pdf format (on the day preceding each lecture). | ||||||||||||||||||||||||||||||||||||||||||||
| Literature | See: www.csms.ethz.ch/education/CSBMS | ||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Since the exercises on the computer do convey and test essentially different skills than those being conveyed during the lectures and tested at the oral exam, the results of the exercises are taken into account when evaluating the results of the exam (learning component, possible bonus of up to 0.25 points on the exam mark). For more information about the lecture: www.csms.ethz.ch/education/CSBMS | ||||||||||||||||||||||||||||||||||||||||||||
| 529-0195-00L | Scientific Information Retrieval & Management in Life Sciences and Chemistry | 2 credits | 2V | O. Renn, L. Betschart, J. Dolenc | |||||||||||||||||||||||||||||||||||||||||
| Abstract | Students learn how to effectively retrieve, critically judge, analyze and manage published scientific information – important skill sets in chemistry and life sciences where scientists need to deal with vast amounts of information. The course, using practical examples, also covers scientific writing, visualizations, science communication and state-of-the-art technologies such as text mining. | ||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Students are made aware about the wide variety of information solutions that exist today for all kinds of research processes, get an independent understanding of how they are derived and learn how to critically judge their quality. They learn how scientific communication works today and on which concepts and principles it is based. They develop the ability to select appropriate, subject-specific databases or tools for a given specific scientific question based on a sound understanding on how a tool or database has been developed and maintained, thus building the personal capacity of doing research effectively and efficiently by integrating scientific information into the research process when needed. Students learn how to evaluate information solutions, to build suitable search strategies and to integrate them in their information workflows. Also, they learn how to effectively communicate their own scientific results using various distribution channels and to measure the impact of their outreach activities. Overall, they gain the ability to perform all steps of the research cycle in a time- and cost-efficient manner, from the research strategy up to writing a first paper and their Ph.D. thesis. | ||||||||||||||||||||||||||||||||||||||||||||
| Content | The course has been primarily designed for Ph.D. students, also for the Life Science Zurich Graduate School, but is also open to Master students. In a series of 12 units, which always include practical examples (for some lectures a notebook is required), the use of scientific information is taught not in a database-centric view but corresponding to the steps through which scientific research is conducted – including the dissemination of scientific results. This is particularly interesting for students who are about to write-up their first paper or thesis. Students will learn about the different types of information resources and tools, get an insight into the numerous databases and tools that exists and how those are built and maintained, enabling them to critically judge the value and trustworthiness of an information resource. Additionally, they will learn how to communicate their own scientific results properly, using also additional measures that are reflected by alternative metrics. The following topics are covered in twelve modules: 1. & 2. The world of scientific publishing: basics, publishing models 3. Searching and retrieving scientific information using search engines and literature databases 4. Searching and retrieving scientific information using subject-specific databases in chemistry and materials science 5. Searching and retrieving scientific information using subject-specific databases in life sciences 6. Tools for analyzing scientific information 7. Tools for managing scientific information and sharing knowledge, including pipelining tools 8. Patents 9. Text (literature) mining 10. Visualizing molecules for lab reports, presentations, posters, and publications 11. Scientific writing, good design & good scientific practice 12. Communicating & analyzing the impact of (your) science | ||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | The slide deck and supplementary materials will be made available in the teaching document repository (ILIAS) after each lecture. | ||||||||||||||||||||||||||||||||||||||||||||
| Literature | Additional literature and reference are provided in the course material. | ||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
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| 529-0549-01L | Case Studies in Process Design I | 3 credits | 3A | G. Guillén Gosálbez, J. Dolenc, U. Fischer | |||||||||||||||||||||||||||||||||||||||||
| Abstract | The focus of part I of the case study course lies on the literature-based comparison of chemical process alternatives. Based on this compilation and selected quantitative as well as qualitative measures, a process assessment and comparison is conducted. A basic flowsheet is then generated, and mass and energy balances are performed to carry out a preliminary economic and environmental assessment. | ||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | - to obtain knowledge about different databases and sources of information - application of the knowledge obtained in lectures to a real problem - problem-oriented problem solving (application of different methods to the same subject) - team work - report writing and presentation techniques | ||||||||||||||||||||||||||||||||||||||||||||
| Content | The focus of part I of the case study course lies on the literature-based comparison of chemical process alternatives. For this purpose, relevant substance data (i.e. physico-chemical, toxicological, safety, and environmental data), as well as information about synthesis routes and technical implementations (i.e. on reaction kinetics; possible separation operations; economic, safety, and environmental aspects), are collected from the literature. Based on this compilation and selected quantitative as well as qualitative measures, a process assessment and comparison is conducted and the most promising process alternative is chosen for further evaluation. For this alternative, a basic flowsheet and mass and energy balances are generated. | ||||||||||||||||||||||||||||||||||||||||||||