IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Building and Using Workflows Within the DE; Phylogenetics.

Slides:



Advertisements
Similar presentations
Extending the iPlant DE: A Phylogenetics Workflow.
Advertisements

Plant Molecular Systematics (Phylogenetics). Systematics classifies species based on similarity of traits and possible mechanisms of evolution, a change.
Comparative genomics Joachim Bargsten February 2012.
Comparative Genomics Bio Informatics Scott Gulledge.
CHAPTER 25 TRACING PHYLOGENY. I. PHYLOGENY AND SYSTEMATICS A.TAXONOMY EMPLOYS A HIERARCHICAL SYSTEM OF CLASSIFICATION  SYSTEMATICS, THE STUDY OF BIOLOGICAL.
Chapter 2 Opener How do we classify organisms?. Figure 2.1 Tracing the path of evolution to Homo sapiens from the universal ancestor of all life.
Classification and Phylogenies Taxonomic categories and taxa Inferring phylogenies –The similarity vs. shared derived character states –Homoplasy –Maximum.
Phylogeny & The Tree of Life. Phylogeny  The evolutionary history of a species or group of species.
The iPlant Collaborative Community Cyberinfrastructure for Life Science Tools and Services Workshop Discovery Environment Overview.
Computing the Tree of Life The University of Texas at Austin Department of Computer Sciences Tandy Warnow.
Biological Diversity and Systematics EEOB Spring Quarter 2002 Weeks 8-11: Fungi and Plants Instructor: Dr. Andrea D. Wolfe, 326 B & Z, 1735 Neil.
Chapter 18.  The science of grouping organisms according to their presumed natural relationships.  ARISTOTLE ◦ First to classify organisms more than.
Classification and Systematics Tracing phylogeny is one of the main goals of systematics, the study of biological diversity in an evolutionary context.
IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Building and Using Workflows Within the DE; Phylogenetics.
Pollen transcript unigene identifier log 2 -fold change Annotation (BLAST) Unigene L. longiflorum chloroplast, complete genome Unigene
Introductory Phylogenetics and the Blue line in DNA Subway Sheldon McKay DNALC, Cold Spring Harbor Laboratory March 28, 2012.
IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Collaborating with iPlant.
IPlant cyberifrastructure to support ecological modeling Presented at the Species Distribution Modeling Group at the American Museum of Natural History.
IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Collaborating with iPlant.
The Future of the iPlant Cyberinfrastructure: Coming Attractions.
Introduction to Phylogenetic Trees
IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Building and Using Workflows Within the DE; Phylogenetics.
Introduction to Bioinformatics Biostatistics & Medical Informatics 576 Computer Sciences 576 Fall 2008 Colin Dewey Dept. of Biostatistics & Medical Informatics.
My-Plant.org A Phylogenetically Structured Social Network Matthew R Hanlon November 13, 2010.
The iPlant Collaborative Community Cyberinfrastructure for Life Science Tools and Services Workshop Discovery Environment Overview.
ARE THESE ALL BEARS? WHICH ONES ARE MORE CLOSELY RELATED?
Chapter 24: Molecular and Genomic Evolution CHAPTER 24 Molecular and Genomic Evolution.
PhyloGrid: a development for a workflow in Phylogeny E. Montes 1, R. Isea 2 and R. Mayo 1 1 CIEMAT, Avda. Complutense, 22, Madrid, Spain 2 Fundación.
The iPlant Collaborative Community Cyberinfrastructure for Life Science Tools and Services Workshop Discovery Environment Overview.
Announcements Urban Forestry data and photos due next week after the break. Reading. Writing assignment due Oct 18. Choose one of the characteristics out.
IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Overview of the iPlant Discovery Environment.
The theory of evolution is supported with the following evidence 1. Fossil record- using relative dating and carbon-14 dating to determine age of extinct.
Build an Automated Workflow Visual Workflow Creator Discovery Environment.
Introduction to Phylogenetic trees Colin Dewey BMI/CS 576 Fall 2015.
Phylogeny & the Tree of Life
Welcome to Class Define the patterns of evolution.
Agenda for 2-13 Complete Short Answer Questions on Unit 6 Review Pollinate Plants and Check on Flies Classification PowerPoint Cladogram Construction and.
PHYLOGENY AND THE TREE OF LIFE CH 26. I. Phylogenies show evolutionary relationships A. Binomial nomenclature: – Genus + species name Homo sapiens.
Classification. Cell Types Cells come in all types of shapes and sizes. Cell Membrane – cells are surrounded by a thin flexible layer Also known as a.
IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Overview of the iPlant Discovery Environment.
Classification.
Phylogeny & Systematics
Classifying the Diversity of Life – Systematics Is the study of the diversity and relationships of organisms, both past and present. – Taxonomy Is the.
IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Overview of the iPlant Discovery Environment.
Chapter 26 Phylogeny and Systematics. Tree of Life Phylogeny – evolutionary history of a species or group - draw information from fossil record - organisms.
IPlant Collaborative Tools and Services Workshop Overview of the iPlant Discovery Environment Sriram Srinivasan.
Introductory Phylogenetic Workflows in the Discovery Environment Sheldon McKay iPlant Collaborative, DNALC, Cold Spring Harbor Laboratory Feb 8, 2012.
IPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Building and Using Workflows Within the DE; Phylogenetics.
Graduate Research with Bioinformatics Research Mentors Nancy Warter-Perez, ECE Robert Vellanoweth Chem and Biochem Fellow Sean Caonguyen 8/20/08.
Taxonomy & Phylogeny. B-5.6 Summarize ways that scientists use data from a variety of sources to investigate and critically analyze aspects of evolutionary.
Students -LL Ch 22 – 24: Due Monday -Trouble in Paradise: Due Tuesday -Galapagos sent -Phones in bin….muted or off…please & thank you.
CyVerse Workshop Discovery Environment Overview. Welcome to the Discovery Environment A Simple Interface to Hundreds of Bioinformatics Apps, Powerful.
Transforming Science Through Data-driven Discovery Workshop Overview Ohio State University MCIC Jason Williams – Lead, CyVerse – Education, Outreach, Training.
Tools and Services Workshop
Joslynn Lee – Data Science Educator
Phylogeny & the Tree of Life
Biological Classification: The science of taxonomy
Endeavour to reconstruct the characters of each hypothetical ancestor.
Overview Bioinformatics: Analyzing biological data using statistics, math modeling, and computer science BLAST = Basic Local Alignment Search Tool Input.
KEY CONCEPT Entire genomes are sequenced, studied, and compared.
Chapter 26 Phylogeny and the Tree of Life
Classification Evolution Unit.
Systematics Systematics is the science of categorizing organisms into like groups and establishing their relationship relative to each other. Eight major.
Chapter 25 – Phylogeny & Systematics
Phylogenetics Chapter 26.
Chapter 25 Essential Questions
Phylogeny & Systematics
Organizing Life's Diversity
Classification Made Easy!
EVOLUTIONARY PROCESSES CREATE DIVERSITY
Presentation transcript:

iPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Building and Using Workflows Within the DE; Phylogenetics

“Knowledge of evolutionary relationships is fundamental to biology, yielding new insights across the plant sciences, from comparative genomics and molecular evolution, to plant development, to the study of adaptation, speciation, community assembly, and ecosystem functioning.” Workflows within the DE; Phylogenetics Why is the Tree of Life Important?

Workflows within the DE; Phylogenetics We like to put things into categories!

Workflows within the DE; Phylogenetics Why is the Tree of Life Important? Midway between the unintelligible and the commonplace, it is metaphor which produces most knowledge. —Aristotle, Rhetoric III

A B C DE F * But not always Workflows within the DE; Phylogenetics Classifications represent inferred evolutionary relationships*

(E) human Consider primates: Do humans make up a monophyletic group? Workflows within the DE; Phylogenetics Classifications represent inferred evolutionary relationships*

Workflows within the DE; Phylogenetics What is a monophyletic group, again?

(E) human Hylobatidae Pongidae Hominidae Workflows within the DE; Phylogenetics Classifications represent inferred evolutionary relationships*

Phylogeny based on globin pseudogene suggests that humans and chimpanzees make up a single monophyletic group outgroup Workflows within the DE; Phylogenetics Classifications represent inferred evolutionary relationships*

How can iPlant help with phylogenetics?

Scalability

Workflows within the DE; Phylogenetics Trees also present computational challenges Number of atoms in the universe

It can take weeks or months to analyze data sets with > 100, 000 species. Example of iPlant contribution: NINJA/WINDJAMMER (Neighbor-Joining) -- NINJA 216K species, ~8 days -- WINDJAMMER 216K species, ~4 hours Workflows within the DE; Phylogenetics Trees also present computational challenges

How can we scale up phylogenetic tree visualization? Goloboff et al Largest Published Tree (73,060 species)

HD TV: 1920 × ,533 names largest computer monitors: 3280×2048 (can be tiled) Laser printer: effectively 3600 × 4725 (can be tiled)

Prototype iPlant tree viewer

Scientific Question: How are ATP Synthase Subunit B (atpB) genes in basal groups of Magnoliophyta species related? Phylogenetic Workflow Lab

ATP Synthase Subunit B gene, Basal Magnoliophyta. Phylogenetic Workflow Lab

Please login to the Discovery Environment. Follow along with the instructor Or Follow along with the handouts on your own

Phylogenetic Workflow Lab Use workflows to simplify your life Extend your research beyond just next-gen sequence analysis Chain together multiple apps and make it easy for your collaborators to copy your exact workflow Future improvements will include branching and decision points that further extend capabilities, such as parameter sweeps

Feedback: Privacy Policy Feedback
Do Not Sell My Personal Information
About project: SlidePlayer Условия использования

© 2024 SlidePlayer.com. Inc. All rights reserved.