410 1.1 Intro Bi 410/510: Introduction Links 1 The Basics 1.1 instructor: John Conery [email protected] 313 Pacific (IE²) MTW 3-4 or by appointment 1.2 web site: http://piazza.com/uoregon/winter2015/bi410510/home syllabus syllabus.pdf project descriptions, resource links, lecture notes [maybe] main use: group discussion 1.3 textbook: Haddock and Dunn, Practical Computing for Biologists (Sinauer), 2011 http://practicalprogramming.org e-book or hard copy 1.4 survey: I’d like to know more about student backgrounds find a link to the survey on Piazza 2 Schedule (Weeks 1 and 2) 2.1 the first project is posted on Piazza https://piazza.com/uoregon/ winter2015/bi410510/resources 2.2 a minor distraction coming up next week…. � lecture period on Jan 12 will be a discussion and help session attendance optional 3 Course Goals 3.1 learn skills required to manage workflows workflow.pdf basic Python programming (reading/writing data, control flow, debugging skills) managing data with SQLite (relational database system) visualization and analysis with R finding, installing useful modules 3.2 For details see “Learning Outcomes” in the syllabus 3.3 Skills will be generally useful, but still “tip of the iceberg” very simple algorithms and data structures use (but not design) objects (“OOP”) nothing about GUIs, data mining, graphics, … 4 What to Expect 4.1 learn to fail 4.2 learn by doing (i.e. practice, practice, practice) 4.3 do the projects! 4.4 don’t postpone until the night before 4 What to Expect 4.1 learn to fail 4.2 learn by doing (i.e. practice, practice, practice) 4.3 do the projects! 4.4Bi don’t410/510: postpone untilIntroduction the night before Links 5 Let’s Get Started 5.1 install Python https://www.python.org the book uses Python 2.7 (many scientific modules) I like (and Python community recommends) Python 3.4 use either version for this class (I’ll try to point out differences) 5.2 find, install a text editor recommendations in PCFB: a) Notepad++ (Windows, also Mac and Linux) http://notepad-plus-plus.org b) TextWrangler (Mac OS X only) http://www.barebones.com c) gedit (Linux, also Windows and Mac) https://wiki.gnome.org/Apps/Gedit see also: http://alternativeto.net Mac users: do not use Text Edit (it works, but….) 5.3 locate your terminal emulator Windows: “Command Prompt” Linux and Mac OS X: “Terminal” 5.4 Windows users only: Cygwin (see Appendix in PCFB) 5.5 Snippet management optional, but highly recommended start a notebook that has little pieces of code (“snippets”) there are apps that help manage snippets, e.g. Quiver for Mac OS X 5.6 more to comer later (sqlite3, RStudio, …).