MODULE 2: Advanced methodologies and tools for research. Research funding and innovation. Code: 43642 Credits: 6 ECTS Type: Compulsory Language: English/Spanish Module s Coordinator: Àlex Sánchez alex.sanchez@vhir.org Schedule for mentoring: Alex Sánchez: Fridays from 15:00 to 17:00h Anaïs González: Fridays from 15:00 to 17:00h. Although having this timetable proposal, the students have to arrange an appointment with the teacher by e mail. Professors responsible for each section: Alex Sánchez Pla alex.sanchez@vhir.org Section I: Biostatistics Anaïs González Anais.gonzalez@vhir.org Section II: Research Funding Raquel Egea Raquel.egea@vhir.org Section III: Innovation [1/7]
OBJECTIVES This module will provide the student with a variety of transversal tools which can be considered essential for research. The Biostatistics and Bioinformatics part will present the main Statistical methods for carrying out data management and data analysis tasks as well as some bioinformatic tools for dealing with high throughput data produced by modern technologies such as microarrays or Next Generation Sequencing. On the other hand, this module will provide the student with knowledge and tools to develop a look for funding strategy. Basic concepts and strategies about write a grant, kind of grants, etc will be explained on the course. Moreover, students will learn about patents, IP and basis of technology transfer process. At the end of the module the student should: Be able to identify the different type of problems that require statistical methods for their analysis Be familiar with the main groups of statistical methods, their applicability conditions and their interpretation. Know how to use some (of the most common) methods using the free statistical language R and R commander. Be familiar with tools such as genomic browsers or Biomart for querying biological information databases Be acquainted of high throughput analysis methodologies and know how to use some user friendly tools such as Galaxy for doing basic processes such as gene selection or exome variant analysis. Be able to identify different grant calls and funding scheme. Have a sound knowledge about funding schemes, rules and grant writing basis. Have basic knowledge about Technology transfer, patents, and innovation. SKILLS E01. Identify and use the concepts, tools, techniques and methodologies for translational biomedical research. E01.1. Identify tools for analysis and management of biomedical data. Databases (BASE) and R. E01.2. Use the programs and statistical tests and interpret the results from a medical and biostatistician point of view. E01.3. Build predictive and analytical models. E01.4. Identify and know how to search in the main bioinformatics resources and databases (NCBI, EBI, ENSEMBL). E01.5. Know the main high performance data types and the techniques and peculiarities for their analysis. E01.6. Identify the role of research centers in terms of innovation and business development. E01.7. Know the terminology and identify the elements of the innovation process, as well as, the main steps of the technology transfer process. E01.8. Develop skills for planning and research project management, both in public and private sector. E01.9. Identify national and international financial systems, as well as the tools to develop winner proposals. [2/7]
CONTENT SECTION I: BIOSTATISTICS 1. Statistical Methods in biomedicine. 1.1. Descriptive Studies. Biological variability. 1.2. Principles of Statistical Inference. Estimation. 1.3. Hypothesis testing. 1.4. Multi Comparison approaches. 2. Experimental design and Analysis of Variance. 2.1. Principles of experimental design. 2.2. Analysis of Variance and its relation with design. 2.3. ANOVA models: Random designs, Block designs, Factorial designs and repeated measures designs. 3. Regression Models in Biomedicine. 3.1. Regression for quantitative outcome variable: Multiple linear regression model. 3.2. Regression for categorical outcome variable: Logistic regression model. 3.3. Regression for count outcome variable: Poisson regression. 3.4. Regression for time to event outcome: Survival analysis and Cox regression model. 4. Statistical methods for Biomarker building and validation. 4.1. Biomarkers: Definition, use, types. 4.2. The biomarker development process. 4.3. Building and validating biomarkers: statistical and bioinformatical approaches. 5. Accessing molecular biology and disease information 5.1. Main sources of biological information 5.2. Querying databases and browsing genomes 5.3. Searching in biological databases using BLAST 6. Introduction to high throughput data analysis 6.1. Gene expression analysis: Microarrays and RNA seq 6.2. Other bioinformatic analyses SECTION II: RESEARCH FUNDING 1. Looking forward the next step: Science or Industry? 2. Competitive funding: 2.1. National: MINECO, AGAUR, La Marató, other national funding entities. 3. International funding: 3.1. Horizon2020 3.2. NIH: 3.3. Private and public foundations: fundraising and some strategies. 4. Writing a proposal: Dirty tips to prepare a successful proposal. 5. Case Study: Writing a grant. [3/7]
SECTION III: INNOVATION 1. Introduction 1.1. Hospitals as a R&D Company 1.2. Hospitals as economic key player 1.3. Health innovation ecosystem 2. The process of valorisations and commercialization; over view of technology transfer 2.1. Methods and process 2.2. Cases 3. Protection of Innovation 3.1. Strategies 3.2. Case 4. Licensing and collaborative projects 4.1. Negotiation. Agreements 4.2. Case 5. Spin off 5.1. Why. The process. Agreement. 5.2. Case METHODOLOGY Biostatistics and bioinformatics session will be divided in two parts: One of theoretical exposure followed by a practical one where students will work in groups of 1 2 in the resolution and discussion of practical situations in real biomedical research analysis. Result will be discussed in the general group. There will be some practical labs to instruct the students on the use of statistical software (R/Rcommander) that will be used later in the course for data analysis. [4/7]
EVALUATION Students work for the biostatistics and bioinformatics part (60%) will be evaluated based on the following criteria: Continuous evaluation will be performed consisting of multiple tag questions based on in class work and explanations. (50%) Participation in discussions, especially on online forums will be encouraged and extra credit may offered for outstanding contributions. Final exam. A final exercise to check the work done by the student will be performed at the end of the sessions. This will mainly consist of practical data analysis exercises and some short multi answer questions (50%). Students work for the Research Funding and Innovation Section (40%) will be evaluated based on the following criteria: Course participation, by contributing to discussions (in place and online). Providing resources when required. (50%) Assessment submission: A draft proposal will be prepare by the students following the instructions and indications provided on the course. Template will be provided first day of the course; and the research subject will be selected by students. (50%) Final Assessment: Biostatistics and bioinformatics Section (60%) + Research Funding and Innovation Section (40%) Regular attendance is compulsory for all the students. Maximum permitted absence: 20% of the classes. TEACHING STAFF Alex Sànchez Santiago Pérez Hoyos Ferran Brianso Xavier de Pedro Miriam Mota Ricardo Gonzalo Anaïs González Esther Arevalo Anne Laure Aslanian Raquel Egea Marco Pugliese Elisabet del Valle Georgina Sorrosal alex.sanchez@vhir.org santi.perezhoyos@vhir.org ferran.brianso@vhir.org xavier.depedro@vhir.org miriam.mota@vhir.org ricardo.gonzalo@vhir.org anais.gonzalez@vhir.org esther.arevalo@vhir.org anne.aslanian@vhir.org raquel.egea@vhir.org marco.pugliese@vhir.org elisabet.delvalle@vhir.org georgina.sorrosal@vhir.org [5/7]
ACADEMIC SCHEDULE Biostatistics & Bioinformatics: from October 9 th to November 5 th 2015. 9 sessions on 9, 13, 14, 15, 16, 23, 29 October and 3, 5 November. From 4 to 8 pm. Classroom 112 Mòdul Sud, Unitat Docent Vall d Hebron UAB Research funding and innovation: from March 29 th to April 4 th 2016 5 sessions (every day) From 3 to 7 pm. Classroom 106 Mòdul Nord, Unitat Docent Vall d Hebron UAB OCTOBER 2015 Monday Tuesday Wednesday Thursday Friday Saturday Sunday 5 6 7 8 9 10 11 M1 M1 M1 M1 M2 12 13 14 15 16 17 18 M2 M2 M2 M2 19 20 21 22 23 24 25 M1 M1 M1 M1 M2 26 27 28 29 30 31 1 M1 M1 M1 M2 M1 NOVEMBER 2015 Monday Tuesday Wednesday Thursday Friday Saturday Sunday 2 3 4 5 6 7 8 M1 M2 M1 M2 M1 MARCH/ APRIL 2016 Monday Tuesday Wednesday Thursday Friday Saturday Sunday 15 19h MÒDUL NORD 28 29 30 31 1 2 3 AULA 106 M2 M2 M2 M2 15 19h MÒDUL NORD AULA 106 M2 4 5 6 7 8 9 10 [6/7]
BIBLIOGRAPHY Rosner, Bernardt (2013). Foundamentals of Biostatistics 7th edition Statistics at Square Two: Understanding Modern Statistical Applications in Medicine Estadistica básica con R y R Commander http://cran.r project.org/doc/contrib/saez Castillo RRCmdrv21.pdf Library resources for Biostatistics: http://libguides.lib.msu.edu/content.php?pid=55914&sid=409145 Apuntes y videos de Bioestadística http://www.bioestadistica.uma.es/baron/apuntes/ Material docente de la Unidad de Bioestadística Clínica del Hospital Ramón y Cajal http://www.hrc.es/bioest/m_docente.html http://grants.nih.gov/grants/grant_tips.htm http://www.cippp.org/pubs/granttip.pdf http://www.timeshighereducation.co.uk/news/tips on writing a winning research proposal forhorizon 2020/2015750.article http://ec.europa.eu/research/participants/portal/desktop/en/home.html http://www.isciii.es/isciii/es/contenidos/fd investigacion/fd financiacion/convocatorias ayudasaccion estrategica salud.shtml http://www10.gencat.cat/agaur_web/appjava/catala/index.jsp http://www.ajutsmarato.com/inici/tabid/218/default.aspx http://ec.europa.eu/research/horizon2020/pdf/press/horizon2020 presentation.pdf http://www.grants.gov/web/grants/home.html https://proposalcentral.altum.com/ [7/7]