The course offers an introduction to programming logic and computational tools for the social sciences graduate students. The course focus on procedures to (1) gather (2) organize and (3) present social data. The course aims to develop programming skills for handling data with academic purposes. Notice that this is not a methods, data analysis or computational social science course. The course is divided in two parts. In the first part we focus on preparing the computational enviroment, getting used with the tools and developing programming literacy in R, Git, SQL, Markdown, and other languages required in class. In the second part we apply the skills acquired in the first part to handle big datasets, webscrapping and third party APIs, digital files management for textual analysis, graphs, maps and other topics of interest. This course aims to fill a gap _common among social science students- providing the training in data management and computational skills Faculty of Philosophy, Languages and Human Sciences (FFLCH) São Paulo main campus 1 – Basics of R Programming 2 – Data structures and data management in R 3 – Tables and graphs in R 4 _ R + SQL basics 5 – Git basics 6 – Markdown basics 7 – LaTex basics 8 – Webscraping 9 – Text, corpus and natural language processing 10 – Maps and GIS 11 – Networks and graphs Glauco Peres da Silva, Leonardo Sangali Barone 40 FLS6397 8 Weekly activities (50%) and a final project (50%). https://www.google.com.br/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=0ahUKEwi3paLQ9tzYAhXBE5AKHdAvBDkQFghfMAk&url=http%3A%2F%2Fwww.ru.nl%2Fpublish%2Fpages%2F798477%2Fstudent_guide_fflch.pdf&usg=AOvVaw1Cv-BPFTbngDpr4qVjQBud

The course aims to introduce students to the main research paradigms in comparative political behavior; and, to advance training in doing original empirical research on political participation, voting, public opinion analysis, etc. in a comparative perspective. Faculty of Philosophy, Languages and Human Sciences (FFLCH) São Paulo main campus Students should have a background in statistical inference (for example, FLS 5028, or a similar course) and multivariate regression analysis (for example, FLS 6183, or a similar course). 1. Participation 2. Values, Issues and Ideological Orientations 3. Partisanship and Voting 4. Attitudes and Political Behavior 5. Representation 6. Performance and the Vote 7. Economic Crisis and Reform 8. Globalization and the Vote Lorena Guadalupe Barberia 40 FLS6403 8 Problem Sets and Quizzes 50% Final Paper 50% https://www.google.com.br/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=0ahUKEwi3paLQ9tzYAhXBE5AKHdAvBDkQFghfMAk&url=http%3A%2F%2Fwww.ru.nl%2Fpublish%2Fpages%2F798477%2Fstudent_guide_fflch.pdf&usg=AOvVaw1Cv-BPFTbngDpr4qVjQBud

A knowledge of how life originated and evolved on Earth is of central importance in historical Sciences (Geology, Biologie, Astrobiologie). To obtain a general view of the interelated processes (geodynamic, climatic, oceanic, biological) involved in the evolution of the early Earth during the first 2.5 Ga of its history (Hadean, Archean, Early Proterozic). Institute of Geosciences (IGc) São Paulo main campus Less than 200 Ma after its formation, the Earth holds all the attributes of a modern Earth (core, protolithosphere, oceans and atmosphere). However, it will take nearly two billion years to shape terrestrial geodynamics and the major bio-geochemical cycles as we know them today. What happened between the two? When and how did the plate tectonics begin? How did life appear on Earth and in what environments? What are the first traces of life? Is there a link between crustal growth, the diversification of microbial life and the evolution of the composition of the atmosphere? Is oxygenation of the atmosphere and oceans of biological or abiotic origin? These are, among others, the questions we will address during this course, as follows: 1) 4.5-4.4 Ga, accretion and differentiation core-mantle, late veneer, formation of the Moon 2) 4.4-4.1 Ga, first zircons, first continents, first oceans 3) Early Earth geodynamics 4) Early Oceans 5) Early atmosphere 6) Early life Marly Babinski, Pascal Andre Marie Philippot 20 GMG5838 4 Oral presentation given by individual students on key scientific issues related to the evolution of the primitive Earth and early Life. A final written exam on http://www.igc.usp.br/index.php?id=101&L=2

The aim of this discipline is to present the students seminal papers of molecular biology. These papers will be analysed from a historical, methodological and scientific perspective. This discipline complements the basic knowledge acquired in regular disciplines of molecular biology. By discussing original articles, the students will analyze in depth the historical context and the methodologies used by the scientists that pave the way of molecular biology. This will ultimately give the students the tools to understand the basis of molecular biology and the development of scientific thought. Biomedical Sciences Institute (ICB) São Paulo main campus Every lecture will be followed by the discussion of an original article. The student will receive a questionnaire that will guide him/her through the reading of the paper, with the help of the instructors. Items to be discussed include the following topics: (1) Structure and function of DNA ; ( 2 ) RNA and the genetic code ; ( 3 ) Advent of genetic engineering and genomics. Carlos Eduardo Winter, Beny Spira 25 ICB5751 8 Written tests will be used to evaluate student progress during the course. https://ww2.icb.usp.br/ing/

Many fields of biological research have changed markedly over the past few years with the rise of high-throughput laboratory techniques such as microarrays, massive nucleic acid sequencing and proteomic technologies. These technical developments have brought forth not only a significant, and still ongoing, change in philosophical outlook, but have also transformed how work in certain fields is performed in the lab _ more specifically, the computer lab. Generation of huge data files that are only useful after extensive computational processing became a frequent task in many biological research groups. Proper training in basic computational concepts and tools that can greatly aid in such endeavors have thus become essential in order to extract all the information that many modern large-scale techniques of biological research can provide. This course’s goal is to provide intensive and advanced training in computer usage on the command-line interface (CLI) for large-scale data analysis. At the end of the course, students from biologically-oriented backgrounds should be able to use the CLI to view, edit, manipulate, and summarize large data files, successfully extracting biological information and insight from the high-throughput analyses that generated those files. Biomedical Sciences Institute (ICB) São Paulo main campus • Introduction to computers and the Unix family of operating systems. • Accessing the shell (Bash), locally or remotely, and Bash basics. • Getting help with man, info, apropos, and Internet search engines. • Moving around the directory tree; finding and executing programs; navigating/understanding the system (memory, disk space etc.). • System structure; file types; user and group permission model; Changing file access (owner, group, permissions). • Standard streams and redirection; piping. • Finding and manipulating files and directories (create, delete, move, copy, rename, append, concatenate etc.). • Describing and summarizing file content (wc, file); getting data into the system (wget, scp, ftp). • Creating, exploring, and sub-setting files. • Comparing, sorting, and editing files. • Compressing and decompressing data (tar, gz, zip etc.). • Basics of regular expressions. • Compiling third-party programs. • Automating the CLI with basic Bash scripting. Jo_o Marcelo Pereira Alves 10 ICB5765 4 The course is structured in short lectures intermingled with class activity sessions, in order to make the course as practice-oriented as possible. In order to better reflect everyday research practice, the most widespread file formats used in the field will also be introduced and used in as many practical examples as possible. The whole course, including exams, takes place in a computer lab. The use of the command-line environment of Unix-like operating systems (such as Mac OS X and Linux-based systems) will be intensively explored, in order to give students all the working knowledge necessary to run most bioinformatics tools and efficiently analyze their output. Avaliation Form: Final grade will be calculated as the weighted average of midterm exam (weight 2), final exam (weight 2), in-class quizzes (weight 1), and practical exercises (weight 3). A passing grade consists of 5.0 or higher final average and at least 75% attendance. Students with regular semester final grades between 3.0 and 4.9 and attendance above 75% can take a supplementary exam, in which case the second final grade will be the average of the final grade above and the supplementary exam. https://ww2.icb.usp.br/ing/

The proposed program includes experimental designs used in the agricultural experimentation whose structure requires special attention due to the methodology applied for the analysis of the obtianed data. Aims to provide a solid methodological basis for the use of models in the analysis of continuous data and in research, involving concepts of matrix algebra and statistical inference, teaching Hasse diagrams, linear models for incomplete data using the theory of mixed models, including the estimation techniques, checking of model fitting, diagnostics, inference and confidence intervals. Luiz de Queiroz College of Agriculture (ESALQ) Piracicaba campus Hasse Diagrams. Unbalanced cross-classifications. Split-plot experiments. Split-Block experiments. Incomplete block designs. Lattice squares. Groups of experiments. Groups of experiments with common treatments (augmented block). Introduction to mixed models. Sonia Maria de Stefano Piedade, Clarice Garcia Borges Demetrio, Taciana Villela Savian 25 LCE5872 8 Evaluation tests and Seminars http://pt.esalq.usp.br/

Systems analysis is a powerful way to explore and analyse the dynamics of interacting entities. In the case of crop health, systems approaches enable understanding the interaction between pests (plant pathogens and pests) and crops. Systems approaches also allow addressing the impact of the environment (e.g., physical: weather, social: human actions, economic, etc.) on these interactions. A broad context for plant health and its management can therefore be envisioned, including for example socio-economic context of production, trade, and policies. To introduce concepts and methods of systems analysis, and their application to the study, analysis, and management of crop health. Students will acquire a broadened understanding of the dynamics and the impact of plant diseases and pests on crop (agricultural) production, as well as on the environment, and on society and the economy. This will be achieved through systems approach techniques, including but not limited to, simulation modelling. Luiz de Queiroz College of Agriculture (ESALQ) Piracicaba campus This course considers crop health  the collective dynamics of diseases and pests as a whole in a crop. Crop health depends on production situations, that is to say, the set of inter-linked environmental, technical, social, and economical factors that determine the context where agricultural production takes place. Understanding the joint evolution of crop health and production situations is important for future plant health professionals. Brazil occupies a very important position in global agricultural and food trade. The course will introduce issues pertaining to global food and agricultural security, and to globalization, because of their implications for crop health. Systems analysis covers a range of techniques that enable exploring and understanding large and complex questions. One of the approaches of systems analysis, mechanistic simulation modelling, will in particular be used as a methodological backbone for the course. Simulation modelling will be introduced and explained in the course. 1  Context of agricultural production and crop health – Introduction to systems analysis and simulation – Examples of production situations and associated crop health syndromes – Illustration of shifts in production situations leading to crop health changes – Introduction to global agriculture, global crop health problems – Introduction to the effects of global changes on agriculture, crop health – Crop health and global food security – General strategies to manage crop health 2 _Systems analysis: introduction and application to crop health – Systems analysis: concepts and methods – Production levels, crop losses – Damage mechanisms caused by pests – Simulation modelling – Management of natural resources – Negative impacts of agriculture – Long-term disease and pest management Armando Bergamin Filho, Laetitia Willocquet, Serge Savary 30 LFT5890 2 The course will be held during 2 weeks in February: first week for classes and second week for practical activities. Presentation of a case study http://pt.esalq.usp.br/

The course aims to put the students in contact with researchers and professionals working in concentration areas of the Program (Clinical Chemistry, Physiopathology and Toxicology) and in related areas with the presentation of seminars on current advanced topics. The faculty includes national and international researchers. The course is offered in the first semester of each year and is mandatory for the all Doctorate students of the Program. This course will permit the students interact with different areas of research making it possible the acquisition of a broad and updated vision of Science in the concentration areas of the Program and in related areas. School of Pharmaceutical Sciences (FCF) S?o Paulo main campus The program will be determined every semester by the invited speakers. Topics will be preferentially include the areas covered by the Program (Clinical Chemistry, Physiopathology and Toxicology) but also related areas. Sabrina Epiphanio 60 FBC5792 1 Course will be taught in Portuguese and English. Participation in class, seminars report, and frequency. http://www.fcf.usp.br/english.php

The course aims to put the students in contact with researchers and professionals working in concentration areas of the Program (Clinical Chemistry, Physiopathology and Toxicology) and in related areas with the presentation of seminars on current advanced topics. The faculty includes national and international researchers. The course is offered in the first semester of each year and is mandatory for the Master and Direct Doctorate students of the Program. This course will permit the students interact with different areas of research making it possible the acquisition of a broad and updated vision of Science in the concentration areas of the Program and in related areas. School of Pharmaceutical Sciences (FCF) S?o Paulo main campus The program will be determined every semester by the invited speakers. Topics will preferentially include the areas covered by the Program (Clinical Chemistry, Physiopathology and Toxicology) but also related areas. Ana Paula de Melo Loureiro, Silvia Berlanga de Moraes Barros 60 FBC5793 1 Course will be taught in Portuguese and English. Participation in class, seminars report, and frequency. http://www.fcf.usp.br/english.php

Many scientific papers are rejected even before they are evaluated by the reviewers. Writing quality and consistent scientific articles can help to reduce this initial rejection in high-impact journals, making the chance for successful publication more effective. Develop skills to write quality scientific reports. School of Pharmaceutical Sciences (FCF) São Paulo main campus Writing the major topics of an article. General advice on writing English and for publication. Article Edition. Practical exemples and writing. Carla Taddei de Castro Neves, Daniel Jay Hoffman 20 FBC5954 1 Article writing. http://www.fcf.usp.br/english.php

Writing is part of Science. Students enrolled in the Graduate Program in Biochemical and Pharmaceutical Technology are of different backgrounds and include pharmacists, biologists, engineers, veterinarians, among others. Nonetheless, all of them have to publish their results. This course focus on preparing original scientific articles. It highlights the importance of publication for an academic career, as well as for scientific development. Basic practices for scientific writing will be provided to stimulate students to publish their results. With this course we intend to increase the number and quality of publications of the students from the Graduate Program in Biochemical and Pharmaceutical Technology, as well as to contribute to the preparation of dissertations and thesis. The course is intended to provide the students with tools to prepare and publish scientific articles, as well as to help with scientific observation, planning and data organizing. Additionally, we expect to promote critical reading of scientific articles and publishing of the results generated by the students during graduate course. The course will also help students in the preparation of dissertations and thesis. School of Pharmaceutical Sciences (FCF) São Paulo main campus Course will include lectures, exercises, case-studies, and practical classes to discuss the manuscripts to be elaborated by each student during the course. 1- Introduction: – Scientific information through the time and the importance of publishing; – Adequate choice of journal for publication; – Types of articles and presentation styles; – Items of each type of article (full paper, short communication and review); – Discussion about Impact Factor (I.S.I. _ Institute for Scientific Information) and journal quality based on Qualis-CAPES classification. 2- The importance of Scientific Reading. Examples of a step-by-step publication process: manuscript preparation, submission, revisions, proof-reading and final article publication. Analysis of accepted and rejected submitted manuscripts. 3- Organizing the results to be published; discussion and objective statement. Preparation of a manuscript outline. 4- Definition of the manuscript title, keywords, authors and affiliations, corresponding author. Study-case of articles published in the journal selected for manuscript submission. 5- Writing of Materials and Methods Section. Units of measurement, precise description of methods. 6- Writing of Results Section. Presentation of figures, tables, flowcharts and schemes. Appropriate Captioning. 7- Writing of Discussion Section. Highlighting the most important results. Identifying and stating the most important findings of the work. 8- Writing of Conclusion Section and the Abstract. Acknowledgements. 9- References and citations. Abbreviations. 10- Writing of an impacting Cover Letter. How to answer the reviewer�fs comments. Adalberto Pessoa Junior, Carlota de Oliveira Rangel Yangui 15 FBT5700 6 Preparation of a manuscript through the course and exercises related to the manuscript preparation. http://www.fcf.usp.br/english.php

Sterilization processes are performed in laboratories, hospitals and industries as the final processing step for preparation of safe critical materials and devices used in the Public Health sector and for pharmaceutical products, in order to preserve products and to ensure their expected shelf-life. A better understanding of sterilization processes (as the choice of sterilizing agent to be used, kinetic parameters determination and biological indicators application) can minimize misunderstandings related to contamination, production and/or processing of these pharmaceuticals devices. This course aims to present the basic concepts and parameters related to sterilization and validation processes, which are responsible to guarantee consistent sterility levels required for obtaining pharmaceutical and medical products. School of Pharmaceutical Sciences (FCF) São Paulo main campus 1. Introduction_- Concepts and application of sterilization. 2. Kinetic parameters: Decimal reduction time (D-value), Relative resistance (z-value), Sterility Assurance Level, Process equivalent time (F value), Q10 parameter and activation energy. 3. Biological and chemical Indicators: main characteristics, types, applications and relationship. 4. Sterilizing agents: Physical, chemical and gaseous agents. 5. Validation processes: definitions and legislation, qualification of installation, operating system qualification_and physical and biological validation. Practical: Application of biological indicators, determination of kinetic parameters Marina Ishii 13 FBT5736 6 Exercises and seminars. http://www.fcf.usp.br/english.php