yw jakartarb20101031
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Talk at Jakarta.rb (Jakarta, Indonesia's ruby user group http://bintangjatuh.com/jakarta-ruby-meetup-october-2010 ) It's a small overview of what's done in genomics & bioinformatics & how ruby helps. Fire ants on genome photos © Romain Libbrecht & Yannick Wurm. All slides remain © Yannick Wurm. Get in touch if you want to use something.
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This document discusses human evolution and recent insights from genomics. It summarizes that Neanderthals were the closest evolutionary relatives to modern humans and lived in Europe and Western Asia until disappearing 30,000 years ago. A draft sequence of the Neanderthal genome from three individuals was presented, composed of over 4 billion nucleotides. Comparisons with five modern human genomes identified regions potentially affected by selection in ancestral modern humans, involving genes related to metabolism, cognition, and skeletal development. Analysis suggests Neanderthals shared more genetic variants with non-Africans, indicating gene flow from Neanderthals into their ancestors occurred before Eurasian groups diverged.
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2015 10-7-11am-reproducible research
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2. Specific approaches and tools recommended are planning for mistakes, automated testing, continuous integration, and using a coding style guide. R and Ruby style guides are provided as examples.
3. The benefits of following such practices are improving productivity, reducing errors, making code easier to read and maintain, and allowing scientists to focus on scientific questions rather than software issues. Reproducible and sustainable software is the overall goal.
2015 10-7-9am regex-functions-loops.key
This document provides an introduction to regular expressions (regex) for text search and pattern matching. It explains that regex allows for powerful text searches beyond simple keywords. Various special symbols and constructs are demonstrated that allow matching complex patterns and variants in text. Examples show matching names, sequences, microsatellite repeats and more with regex. Functions, loops and logical operators in R programming are also briefly covered.
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2015 9-30-sbc361-research methcomm
This document provides an overview and schedule for the course "SBC 361 Research Methods & Comms". The course is a mixture of advanced analytical skills taught in computer labs using the programming language R, and theoretical content covered in lectures and workshops. It includes two workshops on careers in science and popular science writing. Students will complete assignments involving the computer practicals and tutorials, and a mock exam. The schedule details the topics to be covered each week by different professors and teaching staff. It emphasizes the importance of attending classes, completing required work, and doing additional outside reading to succeed in the course.
2015 09-29-sbc322-methods.key
This document discusses computational methods and challenges for genome assembly using next-generation sequencing data. It describes the four main stages of genome assembly as preprocessing filtering, graph construction, graph simplification, and postprocessing filtering. Each stage processes the data from the previous stage to build the assembly graph and reduce complexity, though some assemblers delay filtering steps.
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This document outlines the course SBC322 Ecological and Evolutionary Genomics. It discusses how new genomic technologies have changed ecology and evolution research by merging molecular and ecological approaches. It aims to critically evaluate research questions, methods, experimental designs and applications in ecological and evolutionary genomics. The course will improve students' skills in critically reading literature, understanding interdisciplinary science, and oral and written scientific communication through interactive small group work, informal and formal presentations, blog posts, and peer review.
2015 09-28 bio721 intro
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Introduction to objective, scope and outcome the subject
Chapter 2
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Chapter 3
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Chapter 6
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1. Palancharmy, Basic Civil Engineering, McGraw Hill publishers.
2. Satheesh Gopi, Basic Civil Engineering, Pearson Publishers.
3. Ketki Rangwala Dalal, Essentials of Civil Engineering, Charotar Publishing House.
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