17
Bioinformatics: Software

P0440
Integrated Software GACD for Linkage Map Construction and Gene Mapping in Clonal F1 and Double Cross Populations
Luyan Zhang, Instititue of Crop Sciences, Chinese Academy of Agricultural Sciences; Jiankang Wang, Instititue of Crop Sciences, Chinese Academy of Agricultural Sciences; Lei Meng, Instititue of Crop Sciences, Chinese Academy of Agricultural Sciences; Wencheng Wu, Instititue of Crop Sciences, Chinese Academy of Agricultural Sciences

P0441
GOBII: Genomic Open-source Breeding Informatics Initiative
Philip Glaser, Cornell Institute of Biotechnology; Yanxin Gao, Cornell University; Elizabeth Jones, GOBII Project, Biotechnology Dept, Cornell University; Yaw A. Nti-Addae, Cornell University; Kevin Palis, Boyce Thompson Institute; Syed Raza, Cornell University; Joshua Lamos-Sweeney, Cornell University; Angel Villahoz-Baleta, Cornell University; Kelly Robbins, Cornell University; Jean-Luc Jannink, USDA-ARS; Lukas Mueller, Boyce Thompson Institute; Mark E Sorrells, Cornell University; Qi Sun, Institute for Genomic Diversity, Cornell University; Edward S. Buckler, USDA-ARS-Cornell University; Susan McCouch, Cornell University

P0442
Gigwa - Genotype Investigator for Genome-Wide Analyses
Manuel Ruiz, CIRAD, UMR AGAP / CIAT; Guilhem Sempéré, CIRAD, UMR Intertryp; Adrien Petel, CIRAD; Alexis Dereeper, IRD, UMR RPB; Gautier Sarah, INRA - UMR AGAP; Pierre Larmande, IRD, UMR DIADE, Institut de Biologie Computationnelle

P0443
User-Friendly Whole Genome DNA Methylation Analysis With FlowGe
Jeffrey Grover, University of Arizona; Matthew Bomhoff, University of Arizona; Sean Davey, University of Arizona; Brian D. Gregory, University of Pennsylvania; Rebecca A. Mosher, University of Arizona; Eric Lyons, University of Arizona

P0444
Apollo: Collaborative Manual Genome Annotation with Visual Predictions
Nathan A Dunn, Lawrence Berkeley National Laboratory; Monica C. Munoz-Torres, Lawrence Berkeley National Labs; Deepak Unni, Division of Animal Sciences, University of Missouri; Eric Yao, Department of Bioengineering, Berkeley, CA; Colin Diesh, Division of Animal Sciences, University of Missouri; Ian Holmes, Department of Bioengineering; Christine G. Elsik, Division of Plant Sciences, University of Missouri; Suzanna Lewis, Lawrence Berkeley National Laboratory

P0445
CartograTree Workflows with Tripal API for Association Mapping in Forest Trees
Nic Herndon, University of Connecticut

P0446
EasyMirror and EasyImport: Set up Your Own Ensembl Site in 2 Hours for Your Favourite Taxa
Sujai Kumar, The University of Edinburgh; Richard J Challis, Edinburgh University

P0447
Benchmarking Alignment and Quantification Tools on Plant RNA-Seq Data with CyVerse Cyberinfrastructure
Kapeel Chougule, Cold Spring Harbor Laboratory; Liya Wang, Cold Spring Harbor Laboratory; Joshua Stein, Cold Spring Harbor Laboratory; Doreen Ware, Cold Spring Harbor Laboratory

P0448
KBase: An Open and Extensible Cyberinfrastructure to Accelerate Predictive Systems Biology
Vivek Kumar, Cold Spring Harbor Laboratory; Sunita Kumari, Cold Spring Harbor Laboratory; Jim Thomason, Cold Spring Harbor Laboratory; Doreen Ware, Cold Spring Harbor Laboratory; Nomi Harris, Lawrence Berkeley National Laboratory; Christopher Henry, Argonne National Laboratory; Robert W. Cottingham, Oak Ridge National Laboratory; Adam Arkin, Lawrence Berkeley National Laboratory

P0449
Genome Context Viewer: A User-Friendly Web Application for Visualizing and Mining Shared Gene Content Among Multiple Genomes
Andrew Farmer, National Center for Genome Resources (NCGR); Alan Cleary, Montana State University

P0450
kWIP: The k-Mer Weighted Inner Product, a de novo Estimator of Genetic Similarity
Kevin D. Murray, The Australian National University; Christfried Webers, Data61/CSIRO; Cheng Soon Ong, Data61/CSIRO; Justin O. Borevitz, The Australian National University; Norman Warthmann, The Australian National University

P0451
Exploiting the Great Potential of Sequence Capture Data By a New Tool, SUPER-CAP
Walter Sanseverino, Sequentia Biotech; Riccardo Aiese Cigliano, Sequentia Biotech; Andreu Paytuvi Gallart, Sequentia Biotech; Amalia Barone, University of Naples Federico II; Iratzu Anzar, Sequentia Biotech; Valentino Ruggieri, University of Naples Federico II; Roberta Calafiore, University of Naples Federico II

P0452
BUSCO v2: Assessing Genome Assembly and Annotation Completeness Withbenchmarking Universal Single-Copy Orthologs
Felipe A. Simão, University of Geneva Medical School & Swiss Institute of Bioinformatics; Robert M. Waterhouse, University of Geneva Medical School & Swiss Institute of Bioinformatics; Mathieu Seppey, University of Geneva Medical School & Swiss Institute of Bioinformatics; Panagiotis Ioannidis, University of Geneva Medical School & Swiss Institute of Bioinformatics; Evgenia V. Kriventseva, University of Geneva Medical School & Swiss Institute of Bioinformatics; Evgeny M. Zdobnov, University of Geneva Medical School & Swiss Institute of Bioinformatics

P0453
HiCloud: A Pipeline for a More Inclusive Way to Analyze Hi-C Data
Andreu Paytuví, Sequentia Biotech; Iratzu Anzar, Sequentia Biotech; Covadonga Vara, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona; Walter Sanseverino, Sequentia Biotech; Riccardo Aiese Cigliano, Sequentia Biotech; Aurora Ruiz-Herrera, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona

P0454
Using the Public Plant Breeding API (BrAPI) to Access Data from the Statistical Platform R
Reinhard Simon, International Potato Center (CIP); Nicolas Morales, Boyce Thompson Institute; Maikel Verouden, Biometris, Wageningen Plant Research; Lukas Mueller, Boyce Thompson Institute

P0455
Pathway Visualization Tools in Phytozome
Joseph W. Carlson, DOE Joint Genome Institute; Patrick Davidson, DOE Joint Genome Institute; David M. Goodstein, DOE Joint Genome Institute; Daniel S. Rokhsar, DOE Joint Genome Institute

P0456
Multi-Trait Genome Wide Association Tests Result in a Reduction in False Positives
Anthony Greenberg, Bayesic Research; Jean-Luc Jannink, USDA-ARS; Susan McCouch, Cornell University

P0457
Plant Genome Reannotation Using NextGen Sequences
Shengqiang Shu, DOE Joint Genome Institute; Jerry Jenkins, HudsonAlpha Institute for Biotechnology; David M. Goodstein, DOE Joint Genome Institute; Jeremy Schmutz, Hudson Alpha; Daniel S. Rokhsar, DOE Joint Genome Institute

P0458
Camoco: A Computational Framework for Inter-Relating GWAS Loci and Unraveling Gene Function Using Co-Expression Networks
RJ Schaefer, University of Minnesota; Jean-Michel Michno, Department of Agronomy and Plant Genetics, University of Minnesota; Molly E McCue, University of Minnesota; Brian P. Dilkes, Department of Biochemistry, Purdue University; Ivan Baxter, USDA-ARS, Danforth Plant Science Center; Chad Myers, University of Minnesota

P0459
Selecting Superior de novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome
Loren A Honaas, USDA-ARS Tree Fruit Research Lab; Eric Kenneth Wafula, Penn State University; Norman Wickett, Chicago Botanic Garden; Joshua P. Der, California State University, Fullerton; Yeting Zhang, Rutgers University; Patrick Edger, Department of Horticulture, Michigan State University; Naomi Altman, Penn State; J. Chris Pires, Division of Biological Sciences, University of Missouri; Jim Leebens-Mack, University of Georgia; Claude dePamphilis, Penn State University

P0460
GAPIT3: New Architecture to Quickly Adapt Third Party Packages for Genomic Association and Prediction
Jiabo Wang, Northeast Agricultural University; Zhiwu Zhang, Washington State University

P0461
De novo Assembly of Complete Chloroplast Genomes
Moreland Gibbs, Biomatters, Ltd.; Hilary Miller, Biomatters, Ltd.; Matt Kearse, Biomatters, Ltd.; Helen Shearman, Biomatters, Inc.; Cristina Gamba, Biomatters, ApS.

P0462
A GUI Application "CA Plot Viewer": Large-Scale Gene Expression Network Analysis and Web Databases for Crops
Kentaro Yano, School of Agriculture, Meiji University; Shin Terashima, School of Agriculture, Meiji University; Yukino Nakamura, School of Agriculture, Meiji University; Maasa Kanno, School of Agriculture, Meiji University; Misa Saito, School of Agri., Meiji University; Koji Yokoyama, School of Agriculture, Meiji University; Hajime Ohyanagi, School of Agriculture, Meiji University; Toru Kudo, School of Agriculture, Meiji University; Masaaki Kobayashi, School of Agriculture, Meiji University

P0463
Heap: A Highly Sensitive and Accurate SNP Calling Tool with Low-Coverage High-Throughput Sequencing Data
Masaaki Kobayashi, School of Agriculture, Meiji University; Hajime Ohyanagi, King Abdullah University of Science and Technology; Hideki Takanashi, CREST, JST; Satomi Asano, School of Agriculture, Meiji University; Toru Kudo, School of Agriculture, Meiji University; Hiromi Kajiya-Kanegae, Agricultural and Life Sci., The Univ. of Tokyo; Atsushi J. Nagano, Center for Ecological Research, Kyoto University; Hitoshi Tainaka, CREST, JST; Tsuyoshi Tokunaga, CREST, JST; Takashi Sazuka, Nagoya Univ.; Hiroyoshi Iwata, CREST, JST; Nobuhiro Tsutsumi, CREST, JST; Kentaro Yano, CREST, JST

P0464
solGS: A Webtool for Genomic Selection Analysis
Isaak Y. Tecle, Boyce Thompson Institute; Naama Menda, Boyce Thompson Institute; Guillaume J. Bauchet, Boyce Thompson Institute; Lukas Mueller, Boyce Thompson Institute

P0465
Development of TripalMap
Katheryn Buble, Washington State University; Sook Jung, Washington State University; Jodi L. Humann, Washington State University; Chun-Huai Cheng, Washington State University; Taein Lee, Washington State University; Stephen P. Ficklin, Washington State University; Jing Yu, Washington State University; Dorrie Main, Washington State University

P0466
PhenoApps: Open-Source Android Apps for Phenotyping
Trevor W. Rife, Kansas State University; Jesse Poland, Kansas State University

P0467
GenSAS v5.0: Structural and Functional Annotation Using a Web-Based Platform for Model and Non-Model Organisms
Jodi L. Humann, Washington State University; Stephen P. Ficklin, Washington State University; Taein Lee, Washington State University; Chun-Huai Cheng, Washington State University; Heidi Hough, Washington State University; Sook Jung, Washington State University; Jill L. Wegrzyn, Department of Ecology and Evolutionary Biology - University of Connecticut; David B. Neale, Dept. Plant Sciences University of California Davis; Dorrie Main, Washington State University

P0468
A Software Implementation of a Potato Yield Model to Effectively Support Crop Management and Monitoring
Mario J Caccamo, NIAB; Marc Allison, NIAB; Robert Allen, NIAB; David Legge, NIAB; Christopher Duckett, NIAB; David Firman, NIAB

P0469
TOGGLE-3: A Framework to Build Quickly Pipelines and to Perform Large-Scale NGS Analysis
Christine Tranchant-Dubreuil, IRD - UMR DIADE; Sebastien Ravel, CIRAD; Cécile Monat, IRD - UMR DIADE; Laura Helou, IRD - UMR DIADE; Abdoulaye Diallo, IRD - UMR DIADE; Gautier Sarah, INRA - UMR AGAP; Julie Orjuela-Bouniol, ADNid company; François Sabot, IRD - UMR DIADE

P0470
WISH – Weighted Interaction SNP Hub R Package
Victor Adriano Okstoft Carmelo, Copenhagen University; Lisette J.A. Kogelmann, University of Copenhagen; Haja N. Kadarmideen, University of Copenhagen

P0471
How Interactive Genealogy Graphs Enable to Explore a Hybrid’s Extended Family and Study the Performances of Its Members for Multiple Traits, All within RnDExpTM
David Zinn, Doriane; Tristan Duminil, Doriane; Julie Soula, Doriane; Frédéric Royer, Biosearch Data Management

P0472
Localized Assemblies of the 20 Gbp Sitka Spruce (Picea sitchensis) Genome Using Chromium Reads
Shaun D Jackman, BC Cancer Agency Genome Sciences Centre; Benjamin P Vandervalk, BC Cancer Agency Genome Sciences Centre; René L Warren, Genome Sciences Centre, BC Cancer Agency; Hamid Mohamadi, BC Cancer Agency Genome Sciences Centre; Justin Chu, BC Cancer Agency Genome Sciences Centre; Sarah Yeo, BC Cancer Agency Genome Sciences Centre; Lauren Coombe, BC Cancer Agency Genome Sciences Centre; Stephen Pleasance, BC Cancer Agency Genome Sciences Centre; Robin J Coope, BC Cancer Agency Genome Sciences Centre; Joerg C Bohlmann, University of British Columbia; Steven JM Jones, BC Cancer Agency Genome Sciences Centre; Inanc Birol, BC Cancer Agency Genome Sciences Centre

P0473
Enhancement of Data Searching, Visualization and Exploration in the Hardwood Genomics Database (HGD) by Integration of New Tripal Extensions and Galaxy
Ming Chen, University of Tennessee; Nate Henry, University of Tennessee; Thomas Lane, University of Tennessee; Xiao Zhou, University of Tennessee; Anthony Bretaudeau, INRIA/Irisa - Campus de Beaulieu; Jill L. Wegrzyn, Department of Ecology and Evolutionary Biology - University of Connecticut; Stephen P. Ficklin, Washington State University; Margaret Staton, University of Tennessee

P0474
Exploration and Integration of Multi-Omic Data Using Tools in Agilent GeneSpring
Shweta Shukradas, Agilent Technologies

P0475
VIP: A Functional Annotation Platform of Variants in Animal Genomes
Congcong Liu, Huazhong Agricultural University; Shu-Hong Zhao, Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University; Xuewen Xu, Huazhong Agricultural University

P0476
Integrated Analysis for Genomic Variation, Gene Expression and Gene Regulation
Matthew Keyser, DNASTAR, Inc.

P0477
Fast and Flexible Program for Solving Large Mixed Model Equations
Huimin Kang, China Agricultural University; Lei Zhou, China Agricultural University; Jian-Feng Liu, China Agricultural University

P0478
De novo Assembly and Reconstruction of Complete Circular Chloroplast Genomes using Geneious


P0479
A Novel Tripal Database Module and Workflow to Facilitate Variant Mapping and Detection in Non-Model Plant Species
Qiaoshan Lin, University of Connecticut; Nic Herndon, University of Connecticut; Emily Grau, University of Connecticut; Stephen P. Ficklin, Washington State University; Margaret Staton, University of Tennessee, Knoxville; Sook Jung, Washington State University; Dorrie Main, Washington State University; Alex Feltus, Genetics & Biochemistry, Clemson University; Jill L. Wegrzyn, Department of Ecology and Evolutionary Biology - University of Connecticut

P0480
ADAPTMap and Points Methods for Livestock Digital Phenotyping and Weight Prediction
M.J. Woodward-Greene, USDA-ARS; Clet Wandui Masiga, Association for Strengthening Agricultural Research in Eastern and Central Africa (ASARECA), Entebbe Uganda, current affiliation: Tropical Institute of Development Innovations (TRIDI); Jason M. Kinser, George Mason University; Johann Soelkner, University of Natural Resources and Life Sciences; Tad S. Sonstegard, Acceligen Inc. Animal Ag. Subsidary of Recombinetics; Iosif Vaisman, George Mason University; Curtis P. VanTassell, Animal Genomics and Improvement Laboratory, USDA-ARS

P0481
Core Hunter 3: Flexible Core Subset Selection
Herman De Beukelaer, Ghent University; Guy F Davenport, New Zealand Institute for Plant & Food Research Limited; Veerle Fack, Ghent University

P0482
Discovery and Visualisation of Homologous Genes and Gene Families Using Galaxy
Anil S. Thanki, Earlham Institute; Nicola Soranzo, Earlham Institute; Wilfried Haerty, Earlham Institute; Robert P. Davey, Earlham Institute

P0483
iPat: Interface of Prediction and Association Tools for Genomics
Chun-Peng Chen, Washington State University; Zhiwu Zhang, Washington State University

P0484
Spell-QTL, a Software Suite for QTL Analysis on Modern Datasets
Damien Leroux, MIAT, Institut National de la Recherche Agronomique; Sylvain Jasson, MIAT, Institut National de la Recherche Agronomique

P0485
MMAP:Mining the Maximum Accuracy of Prediction
You Tang, Northeast Agricultural University,china

P0486
Introducing Linkage Map View: An Open Source Tool to Produce Visually Superior Maps in R
Rob Reid, University of North Carolina Charlotte; Cory Brouwer, University of North Carolina at Charlotte; Lisa Ouellette, University of North Carolina Charlotte; Steven Blanchard, University of North Carolina at Charlotte

P0487
Using Intron Position Conservation for Homology-Based Gene Prediction
Jens Keilwagen, Julius Kuehn Institut; Michael Wenk, Institute of Computer Science, Martin Luther University Halle-Wittenberg; Jan Grau, Institute of Computer Science, Martin Luther University Halle-Wittenberg; Jessica Erickson, Martin Luther University Halle-Wittenberg; Martin Schattat, Martin Luther University Halle-Wittenberg; Frank Hartung, Julius Kühn Institut

P0488
Lab7 Enterprise Science Platform: Accelerating Genomic Data Management and Informatics
Christopher Mueller, Lab7 Systems; John Eargle, Lab7 Systems; Cheng Lee, Lab7 Systems; Varshal Dave, Lab7 Systems

P0489
Web-Based Bioinformatics Workflows for RNA-Seq Data Analysis in Agricultural Animal Species
Yuanyuan Chang, J Craig Venter Institute; Alexander Richter, J Craig Venter Institute; Yunsup Jung, J Craig Venter Institute; Qiyun Zhu, J Craig Venter Institute; Robert W. Li, ARS, USDA; Weizhong Li, J Craig Venter Institute

P0490
AIR - Artificial Intelligence RNAseq
Riccardo Aiese Cigliano, Sequentia Biotech; Andreu Paytuvi Gallart, Sequentia Biotech; Ermanno Battista, Sequentia Biotech; Fabio Scippacercola, Sequentia Biotech; Walter Sanseverino, Sequentia Biotech

P1192
Development of an Integrated Breeding System for Genomics-Based Crop Improvement
Yeisoo Yu, Phyzen; Beom-Soon Choi, Phyzen Genomics Institute

P1248
Gtracks: A Framework for Creating and Maintaining UCSC Track Databases Using Google Spreadsheets
Kathleen E. Kyle, Center for Genomics and Personalized Medicine, Florida State University; Hank W. Bass, Department of Biological Science, Florida State University; Daniel L. Vera, Center for Genomics and Personalized Medicine, Florida State University

P1249
Amaryllis Sequencing Index Compatibility Tool (sicTool): Easy, Safe, and Efficient Multiplexed Sequencing
Michael F. Covington, Amaryllis Nucleics

P1260
JBrowse - Javascript Genome Browser
Eric Yao, Department of Bioengineering, Berkeley, CA; Nathan A Dunn, Lawrence Berkeley National Laboratory; Deepak Unni, Division of Animal Sciences, University of Missouri; Robert Buels, Boyce Thompson Institute for Plant Research; Eric Rasche, Texas A & M University; Colin Diesh, Division of Animal Sciences, University of Missouri; Scott Cain, Ontario Institute for Cancer Research; Christine G. Elsik, Division of Animal Sciences, University of Missouri; Monica C. Munoz-Torres, Lawrence Berkeley National Laboratory; Lincoln Stein, Ontario Institute of Cancer Research; Suzanna Lewis, Lawrence Berkeley National Laboratory; Ian Holmes, Department of Bioengineering

P1263
LTR_Retriever: A Highly Sensitive and Accurate Program for Identification of LTR Retrotransposons
Shujun Ou, Michigan State University

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