{ "metadata": { "name": "", "signature": "sha256:68e8fb3e08a2dd744ad23d05e1444a85e91fed64bbdca232ae13041c952ace43" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "What I learned at PAGXXII" ] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Friday" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![summ](files/img/agen-3.png)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![agenda](files/img/agen.png)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Summary- Interesting insight from Birney; next step is reports from session to Scientific Committee where they will outline a white paper\n", "\n", "###Notes" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![notes](http://eagle.fish.washington.edu/cnidarian/skitch/agencode.png)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![notes](http://eagle.fish.washington.edu/cnidarian/skitch/agencode2.png)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![notes](http://eagle.fish.washington.edu/cnidarian/skitch/agencode3.png)" ] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Saturday - Aquaculture Workshop" ] }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Date: Saturday, January 11, 2014 \n", "Time: 8:00 AM-6:10 PM\n", "Room: Royal Palm Salons 3-4\n", "Organizer:\n", "Steven Roberts\n", "8:00 AM\n", "Welcoming Remarks \n", "\n", "\n", "8:15 AM W036\n", "A Genome Map for a Species with Male Tetrasomic Inheritance, Coho Salmon, and Location of Quantitative Trait Loci \n", "Miyako Kodama, University of Washington; Marine Brieuc, University of Washington; Robert Devlin, Fisheries and Oceans Canada; Jeff Hard, Northwest Fisheries Science Center; Kerry Naish, University of Washington \n", "\n", "8:30 AM W037\n", "Genomic Regions Potentially Under Selection in a Hybridized Population of Westslope Cutthroat Trout (Oncorhynchus clarkii Lewisi) \n", "Daniel P. Drinan, University of Washington \n", "\n", "8:45 AM W038\n", "Transcriptome Assembly and Digital Gene Expression Atlas of the Rainbow Trout \n", "Bam D Paneru, Middle Tennessee State University \n", "\n", "9:00 AM W039\n", "Genomic Selection Applied to Pisciricketsia salmonis Resistance in Chilean Atlantic Salmon \n", "Victor Martinez, FAVET-INBIOGEN. University of Chile \n", "\n", "9:15 AM W040\n", "Bulk Segregant RNA-Seq Reveals Expression and Positional Candidate Genes and Allele-Specific Expression for Disease Resistance Against Enteric Septicemia of Catfish \n", "Ruijia Wang, The Fish Molecular Genetics and Biotechnology Laboratory; Luyang Sun, The Fish Molecular Genetics and Biotechnology Laboratory; Lisui Bao, The Fish Molecular Genetics and Biotechnology Laboratory; Jiaren Zhang, The Fish Molecular Genetics and Biotechnology Laboratory; Yanliang Jiang, The Fish Molecular Genetics and Biotechnology Laboratory; Jun Yao, The Fish Molecular Genetics and Biotechnology Laboratory; Lin Song, The Fish Molecular Genetics and Biotechnology Laboratory; Jianbin Feng, The Fish Molecular Genetics and Biotechnology Laboratory; Shikai Liu, The Fish Molecular Genetics and Biotechnology Laboratory; John Liu, The Fish Molecular Genetics and Biotechnology Laboratory \n", "\n", "9:30 AM W041\n", "Dietary Conditioning in Poultry By Limiting Specific Nutrients Early in Life Involves Altered DNA Methylation \n", "\n", "\n", "10:20 AM\n", "Break \n", "\n", "\n", "10:35 AM W042\n", "How Aquaculture Research and Development Could Contribute to Food Security in Developing Countries: Finding Solutions to Agricultural Problems That Affect People Everyday, from Field to Table \n", "\n", "\n", "10:50 AM W043\n", "Genome Dynamism in a Basal Vertebrate: Challenges and Biological Implications \n", "Chris Amemiya, Benaroya Research Institute; Jeramiah J. Smith, University of Kentucky \n", "\n", "11:40 AM\n", "Lunch \n", "\n", "\n", "1:10 PM W044\n", "Developing Molecular Markers for Population and Quantitative Genetic Analysis of Seriola lalandi Using Transcriptome Sequencing \n", "Victor Martinez, FAVET-INBIOGEN. University of Chile; Alok Patel, FAVET-INBIOGEN. UNIVERSIDAD DE CHILE \n", "\n", "1:25 PM W045\n", "A Comprehensive Methylome for Crassostrea gigas Provides Insight into the Role of DNA Methylation in Bivalves \n", "Mackenzie Gavery, University of Washington; Steven Roberts, University of Washington \n", "\n", "1:40 PM W046\n", "Evaluating the Effectiveness of Managed Gene Flow to Reduce Adaptation to Captivity in Supportive Breeding Programs \n", "Charles D. Waters, University of Washington; Marine S. O. Brieuc, University of Washington; Curtis M. Knudsen, Oncorh Consulting; David E. Fast, Yakama Nation Fisheries; Jeff Hard, Northwest Fisheries Science Center; Kenneth I. Warheit, Washington Department of Fish and Wildlife; Kerry Naish, University of Washington \n", "\n", "1:55 PM W047\n", "A Dense Linkage Map for Chinook Salmon (Oncorhynchus tshawytscha) Reveals Variable Chromosomal Divergence Following an Ancestral Whole Genome Duplication Event \n", "Marine S.O. Brieuc, University of Washington; Charles D. Waters, University of Washington; James E. Seeb, University of Washington; Kerry A. Naish, University of Washington \n", "\n", "2:10 PM W048\n", "Microbial and Tissue-Specific Regulation of Gene Transcription in the Zebrafish Intestine \n", "John F. Rawls, Duke University \n", "\n", "3:00 PM\n", "Intermission \n", "\n", "\n", "3:15 PM W049\n", "Tissue\u2010Specific Alternative Splicing in Rainbow Trout \n", "Rafet Al-Tobasei, Middle Tennessee State University \n", "\n", "3:30 PM W050\n", "Atlantic Salmon Liver Transcriptome Response to Diets Containing Camelina Products \n", "Xi Xue, Memorial University of Newfoundland; Tiago S. Hori, Memorial University of Newfoundland; Marije Booman, Memorial University of Newfoundland; Stefanie M. Hixson, Memorial University of Newfoundland; Christopher C. Parrish, Memorial University of Newfoundland; Kim Johnstone, Genome Atlantic; Derek M. Anderson, Dalhousie Agricultural Campus; Matthew L. Rise, Memorial University of Newfoundland \n", "\n", "3:45 PM W051\n", "SNP Discovery in Blue Catfish (Ictalurus furcatus) Populations via Genotyping\u2013by-Sequencing \n", "Eric Peatman, Auburn University; Chao Li, Auburn University; Wilawan Thongda, Auburn University; Benjamin Beck, USDA-ARS Stuttgart National Aquaculture Research Center; Brian Bosworth, USDA-ARS Warmwater Aquaculture Research Unit; Geoff Waldbieser, USDA-ARS Warmwater Aquaculture Research Unit \n", "\n", "4:00 PM W052\n", "Characterization of Rainbow Trout (Oncorhynchus mykiss) Spleen Transcriptome and Identification of Immune-Related Genes \n", "Ali R. Ali, Middle Tennessee State University \n", "\n", "4:15 PM W053\n", "Influence of Camelina Oil-Containing Diets on the Atlantic Cod Antiviral Immune Transcriptome and Elovl Family Transcript Expression \n", "Matthew L. Rise, Memorial University of Newfoundland; Marije Booman, Memorial University of Newfoundland; Xi Xue, Memorial University of Newfoundland; Qingheng Xu, Memorial University of Newfoundland; Stefanie M. Hixson, Memorial University of Newfoundland; Christopher C. Parrish, Memorial University of Newfoundland; Kim Johnstone, Genome Atlantic; Charles Y. Feng, Memorial University of Newfoundland; Derek M. Anderson, Dalhousie Agricultural Campus \n", "\n", "4:30 PM\n", "NRSP-8 Bioinformatics coordinator - Reecy \n", "\n", "\n", "4:45 PM\n", "AgEncode " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "###Notes\n", "![aq](http://eagle.fish.washington.edu/cnidarian/skitch/aq.png)" ] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Sunday" ] }, { "cell_type": "heading", "level": 4, "metadata": {}, "source": [ "AM EBI" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**This session will introduce a number of key bioinformatic resources either hosted at, or contributed to by, the European Bioinformatics Institute and made freely available to the user community**. The featured resources have been selected as being key to genome annotation and analysis.\n", "Date: Sunday, January 12, 2014 \n", " \n", "Time: 8:00 AM-12:40 PM\n", "Room: California\n", "Organizer:\n", "Sandra Orchard\n", "8:00 AM W357\n", "Introduction to Public Domain Resources at the EBI \n", "Sandra Orchard, EMBL-EBI \n", "\n", "8:15 AM W358\n", "Genome Resources at the EBI - Ensembl and Ensembl Genomes \n", "Bert Overduin, European Bioinformatics Institute (EMBL-EBI); Ensembl Team, N/A; Ensembl Genomes Team, N/A \n", "\n", "9:15 AM W359\n", "The Vertebrate Genome Annotation Database (VEGA) and the Use of Otterlace As a Community Annotation Tool \n", "Jane Loveland, Wellcome Trust Sanger Institute \n", "\n", "9:45 AM W360\n", "Expert Curation in UniProtKB \n", "Michel Schneider, Swiss Institute of Bioinformatics; UniProt Consortium, n/a \n", "\n", "10:15 AM W361\n", "The UniProt-Gene Ontology Annotation (UniProt-GOA) Project: Central Resource for Multi-Species GO Annotation \n", "Rachael Huntley, EMBL-EBI \n", "\n", "10:45 AM W362\n", "Automatic Annotation of New Genomes \n", "Sandra Orchard, EMBL-EBI \n", "\n", "11:15 AM W363\n", "Functional Genomics Data and Expression look-up tools: ArrayExpress and new Expression Atlas \n", "Amy Tang, EMBL-European Bioinformatics Institute \n", "\n", "11:45 AM W364\n", "Train Online: Web-Based Learning for Life Scientists \n", "Katrina Costa, EMBL-EBI \n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "###Notes\n", "Genome annotations\n", "Stand 303\n", "\n", "\n", "Bert overduin\n", "Genome resources \n", "Ensembl AND ensembl Genome\n", "\n", "**Oyster genome browser** \n", "\n", "\n", "_Rest api_\n", "There is one for ensembl gen\n", "Consul\n", "Gets url\n", "Awesome\n", "Try\n", "\n", "**Train online !!!**\n", "\n", "\n", "\n", "Goa annotations\n", "\n", "Extended go annotation new\n", "\n", "amigo blast\n", "Blast2go\n", "\n", "\n", "Interproscan\n", "\n", "Neurolex . org\n", "\n", "Quick go should have slim\n", "\n", "----\n", "interpro and interproscan\n", "Hyak\n", "\n", "Array express\n", "\n", "Co- expression \n", "Epistatic network\n", "\n", "\n", "\n", "Programattic access at\n", "Array express\n", "Rest\n", "\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "###More talks \n", "\n", "Networks. Toni Reverter\n", "Pcit algorithm\n", "Seems like tf is important \n", "\n", "Animal tf DATABASE\n", "\n", "\n", "Gorilla\n" ] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Monday" ] }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": [ "AM Posters!! " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"2014-01-13_07_51_02_jpg_188EA296_png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"2014-01-13_07_54_34_jpg_188EA2F1_png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "For above poster " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"2014-01-13_07_57_59_jpg_and_2014-01-13_07_54_40_jpg_188EA3BF.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"2014-01-13_07_58_53_jpg_and_2014-01-13_07_57_59_jpg_188EA41C_png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Galaxy___RepeatExplorer_188EA49F_png\"/\n", "\n", "\n", "---" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"2014-01-13_08_23_24_jpg_188EA594_png\"/" ] }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": [ "Poster EmbryoGENE\n" ] }, { "cell_type": "code", "collapsed": false, "input": [ "from IPython.display import YouTubeVideo\n", "#An overview of the EmbryoGENE platforms for those visiting my PAG XXII poster in my absence.\n", "YouTubeVideo('lZnnq1APceI')" ], "language": "python", "metadata": {}, "outputs": [ { "html": [ "\n", " \n", " " ], "metadata": {}, "output_type": "pyout", "prompt_number": 9, "text": [ "" ] } ], "prompt_number": 9 }, { "cell_type": "markdown", "metadata": {}, "source": [ "High resolution figures\n", "" ] }, { "cell_type": "code", "collapsed": false, "input": [ "from IPython.display import YouTubeVideo\n", "# A presentation of the EmbryoGENE transcriptomic platform by Dr Claude Robert.\n", "YouTubeVideo('ble2V8d5WdQ')" ], "language": "python", "metadata": {}, "outputs": [ { "html": [ "\n", " \n", " " ], "metadata": {}, "output_type": "pyout", "prompt_number": 8, "text": [ "" ] } ], "prompt_number": 8 }, { "cell_type": "code", "collapsed": false, "input": [ "from IPython.display import YouTubeVideo\n", "# A presentation of the EmbryioGENE epigenetic platform by Dr Claude Robert.\n", "YouTubeVideo('MVMQAMiihpw')" ], "language": "python", "metadata": {}, "outputs": [ { "html": [ "\n", " \n", " " ], "metadata": {}, "output_type": "pyout", "prompt_number": 7, "text": [ "" ] } ], "prompt_number": 7 }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"2014-01-13_13_08_56_jpg_188DF4CA_png\"/" ] }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }