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Gene Prediction: the End of the Beginning Comment Colin Semple
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central http://genomebiology.com/2000/1/2/reports/4012.1 Meeting report Gene prediction: the end of the beginning comment Colin Semple Address: Department of Medical Sciences, Molecular Medicine Centre, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK. E-mail: [email protected] Published: 28 July 2000 reviews Genome Biology 2000, 1(2):reports4012.1–4012.3 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2000/1/2/reports/4012 © GenomeBiology.com (Print ISSN 1465-6906; Online ISSN 1465-6914) Reducing genomes to genes reports A report from the conference entitled Genome Based Gene All ab initio gene prediction programs have to balance sensi- Structure Determination, Hinxton, UK, 1-2 June, 2000, tivity against accuracy. It is often only possible to detect all organised by the European Bioinformatics Institute (EBI). the real exons present in a sequence at the expense of detect- ing many false ones. Alternatively, one may accept only pre- dictions scoring above a more stringent threshold but lose The draft sequence of the human genome will become avail- those real exons that have lower scores. The trick is to try and able later this year. For some time now it has been accepted increase accuracy without any large loss of sensitivity; this deposited research that this will mark a beginning rather than an end. A vast can be done by comparing the prediction with additional, amount of work will remain to be done, from detailing independent evidence. -
The EMBL-European Bioinformatics Institute the Hub for Bioinformatics in Europe
The EMBL-European Bioinformatics Institute The hub for bioinformatics in Europe Blaise T.F. Alako, PhD [email protected] www.ebi.ac.uk What is EMBL-EBI? • Part of the European Molecular Biology Laboratory • International, non-profit research institute • Europe’s hub for biological data, services and research The European Molecular Biology Laboratory Heidelberg Hamburg Hinxton, Cambridge Basic research Structural biology Bioinformatics Administration Grenoble Monterotondo, Rome EMBO EMBL staff: 1500 people Structural biology Mouse biology >60 nationalities EMBL member states Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom Associate member state: Australia Who we are ~500 members of staff ~400 work in services & support >53 nationalities ~120 focus on basic research EMBL-EBI’s mission • Provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress • Contribute to the advancement of biology through basic investigator-driven research in bioinformatics • Provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators • Help disseminate cutting-edge technologies to industry • Coordinate biological data provision throughout Europe Services Data and tools for molecular life science www.ebi.ac.uk/services Browse our services 9 What services do we provide? Labs around the -
Functional Effects Detailed Research Plan
GeCIP Detailed Research Plan Form Background The Genomics England Clinical Interpretation Partnership (GeCIP) brings together researchers, clinicians and trainees from both academia and the NHS to analyse, refine and make new discoveries from the data from the 100,000 Genomes Project. The aims of the partnerships are: 1. To optimise: • clinical data and sample collection • clinical reporting • data validation and interpretation. 2. To improve understanding of the implications of genomic findings and improve the accuracy and reliability of information fed back to patients. To add to knowledge of the genetic basis of disease. 3. To provide a sustainable thriving training environment. The initial wave of GeCIP domains was announced in June 2015 following a first round of applications in January 2015. On the 18th June 2015 we invited the inaugurated GeCIP domains to develop more detailed research plans working closely with Genomics England. These will be used to ensure that the plans are complimentary and add real value across the GeCIP portfolio and address the aims and objectives of the 100,000 Genomes Project. They will be shared with the MRC, Wellcome Trust, NIHR and Cancer Research UK as existing members of the GeCIP Board to give advance warning and manage funding requests to maximise the funds available to each domain. However, formal applications will then be required to be submitted to individual funders. They will allow Genomics England to plan shared core analyses and the required research and computing infrastructure to support the proposed research. They will also form the basis of assessment by the Project’s Access Review Committee, to permit access to data. -
Martian Crater Morphology
ANALYSIS OF THE DEPTH-DIAMETER RELATIONSHIP OF MARTIAN CRATERS A Capstone Experience Thesis Presented by Jared Howenstine Completion Date: May 2006 Approved By: Professor M. Darby Dyar, Astronomy Professor Christopher Condit, Geology Professor Judith Young, Astronomy Abstract Title: Analysis of the Depth-Diameter Relationship of Martian Craters Author: Jared Howenstine, Astronomy Approved By: Judith Young, Astronomy Approved By: M. Darby Dyar, Astronomy Approved By: Christopher Condit, Geology CE Type: Departmental Honors Project Using a gridded version of maritan topography with the computer program Gridview, this project studied the depth-diameter relationship of martian impact craters. The work encompasses 361 profiles of impacts with diameters larger than 15 kilometers and is a continuation of work that was started at the Lunar and Planetary Institute in Houston, Texas under the guidance of Dr. Walter S. Keifer. Using the most ‘pristine,’ or deepest craters in the data a depth-diameter relationship was determined: d = 0.610D 0.327 , where d is the depth of the crater and D is the diameter of the crater, both in kilometers. This relationship can then be used to estimate the theoretical depth of any impact radius, and therefore can be used to estimate the pristine shape of the crater. With a depth-diameter ratio for a particular crater, the measured depth can then be compared to this theoretical value and an estimate of the amount of material within the crater, or fill, can then be calculated. The data includes 140 named impact craters, 3 basins, and 218 other impacts. The named data encompasses all named impact structures of greater than 100 kilometers in diameter. -
The Pancam Instrument for the Exomars Rover
ASTROBIOLOGY ExoMars Rover Mission Volume 17, Numbers 6 and 7, 2017 Mary Ann Liebert, Inc. DOI: 10.1089/ast.2016.1548 The PanCam Instrument for the ExoMars Rover A.J. Coates,1,2 R. Jaumann,3 A.D. Griffiths,1,2 C.E. Leff,1,2 N. Schmitz,3 J.-L. Josset,4 G. Paar,5 M. Gunn,6 E. Hauber,3 C.R. Cousins,7 R.E. Cross,6 P. Grindrod,2,8 J.C. Bridges,9 M. Balme,10 S. Gupta,11 I.A. Crawford,2,8 P. Irwin,12 R. Stabbins,1,2 D. Tirsch,3 J.L. Vago,13 T. Theodorou,1,2 M. Caballo-Perucha,5 G.R. Osinski,14 and the PanCam Team Abstract The scientific objectives of the ExoMars rover are designed to answer several key questions in the search for life on Mars. In particular, the unique subsurface drill will address some of these, such as the possible existence and stability of subsurface organics. PanCam will establish the surface geological and morphological context for the mission, working in collaboration with other context instruments. Here, we describe the PanCam scientific objectives in geology, atmospheric science, and 3-D vision. We discuss the design of PanCam, which includes a stereo pair of Wide Angle Cameras (WACs), each of which has an 11-position filter wheel and a High Resolution Camera (HRC) for high-resolution investigations of rock texture at a distance. The cameras and electronics are housed in an optical bench that provides the mechanical interface to the rover mast and a planetary protection barrier. -
Download Final Programme
Session Overview Saturday 17 September 2011 11:15 - 13:15 Arrival and Registration ATC Main Entrance 13:15 - 13:30 Welcome and Opening Remarks Klaus Tschira Auditorium 13:30 - 18:00 Session 1: Somatic Genetics I Chaired by David Tuveson and Ewan Birney Klaus Tschira Auditorium 18:00 - 19:00 Keynote Lecture: Lynda Chin Klaus Tschira Auditorium 19:00 - 20:30 Dinner ATC Canteen Sunday 18 September 2011 09:00 - 12:30 Session 2: Somatic Genetics II / Epigenetics Chaired by James R. Downing Klaus Tschira Auditorium 12:30 - 14:30 Poster Session I and Lunch ATC Foyer and Helix A 14:30 - 18:30 Session 3: Mouse Genetics Chaired by Lynda Chin Klaus Tschira Auditorium 18:30 - 23:00 Gala Dinner and Live Music ATC Canteen and ATC Rooftop Lounge Page 1 EMBO|EMBL Symposium: Cancer Genomics Monday 19 September 2011 09:00 - 13:00 Session 4: Computational Chaired by Peter Lichter Klaus Tschira Auditorium 13:00 - 15:00 Poster Session II and Lunch ATC Foyer and Helix A 15:00 - 16:00 Session 5: Somatic Genetics III Chaired by Andy Futreal Klaus Tschira Auditorium 16:00 - 17:00 Keynote Lecture: Michael Stratton Klaus Tschira Auditorium 17:00 - 17:15 Closing Remarks and Poster Prize Klaus Tschira Auditorium Page 2 Programme Saturday 17 September 2011 11:15 - 13:15 Arrival and Registration ATC Main Entrance 13:15 - 13:30 Welcome and Opening Remarks Klaus Tschira Auditorium 13:30 - 18:00 Session 1: Somatic Genetics I Chaired by David Tuveson and Ewan Birney Klaus Tschira Auditorium 13:30 - 14:00 Somatic genomic alterations in chronic lymphocytic 1 leukemia Elias -
Mars Surface Context Cameras Past, Present, and Future 10.1002/2016EA000166 M
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Aberystwyth Research Portal Aberystwyth University Mars surface context cameras past, present and future Gunn, Matthew; Cousins, Claire Published in: Earth and Space Science DOI: 10.1002/2016EA000166 Publication date: 2016 Citation for published version (APA): Gunn, M., & Cousins, C. (2016). Mars surface context cameras past, present and future. Earth and Space Science, 3(4), 144-162. https://doi.org/10.1002/2016EA000166 Document License CC BY-NC-ND General rights Copyright and moral rights for the publications made accessible in the Aberystwyth Research Portal (the Institutional Repository) are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the Aberystwyth Research Portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the Aberystwyth Research Portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. tel: +44 1970 62 2400 email: [email protected] Download date: 09. Jul. 2020 PUBLICATIONS Earth and Space Science REVIEW Mars surface context cameras past, present, and future 10.1002/2016EA000166 M. D. Gunn1 and C. R. Cousins2 Key Points: 1Institute of Maths, Physics and Computer Science, Aberystwyth University, Aberystwyth, UK, 2Department of Earth and • Camera systems have been a core component of all instrument payloads Environmental Sciences, Irvine Building, University of St Andrews, St. -
Appendix I Lunar and Martian Nomenclature
APPENDIX I LUNAR AND MARTIAN NOMENCLATURE LUNAR AND MARTIAN NOMENCLATURE A large number of names of craters and other features on the Moon and Mars, were accepted by the IAU General Assemblies X (Moscow, 1958), XI (Berkeley, 1961), XII (Hamburg, 1964), XIV (Brighton, 1970), and XV (Sydney, 1973). The names were suggested by the appropriate IAU Commissions (16 and 17). In particular the Lunar names accepted at the XIVth and XVth General Assemblies were recommended by the 'Working Group on Lunar Nomenclature' under the Chairmanship of Dr D. H. Menzel. The Martian names were suggested by the 'Working Group on Martian Nomenclature' under the Chairmanship of Dr G. de Vaucouleurs. At the XVth General Assembly a new 'Working Group on Planetary System Nomenclature' was formed (Chairman: Dr P. M. Millman) comprising various Task Groups, one for each particular subject. For further references see: [AU Trans. X, 259-263, 1960; XIB, 236-238, 1962; Xlffi, 203-204, 1966; xnffi, 99-105, 1968; XIVB, 63, 129, 139, 1971; Space Sci. Rev. 12, 136-186, 1971. Because at the recent General Assemblies some small changes, or corrections, were made, the complete list of Lunar and Martian Topographic Features is published here. Table 1 Lunar Craters Abbe 58S,174E Balboa 19N,83W Abbot 6N,55E Baldet 54S, 151W Abel 34S,85E Balmer 20S,70E Abul Wafa 2N,ll7E Banachiewicz 5N,80E Adams 32S,69E Banting 26N,16E Aitken 17S,173E Barbier 248, 158E AI-Biruni 18N,93E Barnard 30S,86E Alden 24S, lllE Barringer 29S,151W Aldrin I.4N,22.1E Bartels 24N,90W Alekhin 68S,131W Becquerei -
Exomars Presentation
EE XX OO MM AA RR SS Mission Objectives & Science Strategy J. L. Vago and the ExoMars project team Solar System Working Group – SSWG 8 September 2005, ESA HQ (F) The Aurora Programme ESA’s new programme to prepare for the human exploration of the Solar system. Characteristics: Defines a long-term space exploration strategy for Europe; Focuses on exploration infrastructure and technology development; Robotic missions in preparation of future human ones; Synergy between scientific and technological objectives; Provides a framework for cooperation with other space agencies. 2 What is ExoMars? • Is the first mission of ESA’s Aurora Exploration Programme. • ExoMars will deploy two science elements on the Martian surface: a Rover carrying the Pasteur payload, and a fixed station —the Geophysics/Environment Package (GEP). Scientific Objectives: Pasteur Rover: ¾ To search for traces of past and present life on Mars; ¾ To characterise, in the shallow subsurface, vertical distribution profiles for water and geochemical composition. GEP: ¾ To measure planetary geophysics parameters important to understand Mars’s evolution and habitability; ¾ To study the surface environment and identify hazards to human missions. Technology Objectives: To develop a European capability to land large payloads on Mars; To demonstrate high surface mobility and access to the subsurface; 3 To prepare technologies necessary for a Mars Sample Return mission. Why life on Mars? • Early in the history of Mars, liquid water was present on its surface; • Some of the processes considered important for the origin of life on Earth may have also been present on early Mars; • Asteroid and comet impacts may have been less severe on Mars, favouring the survival of life; • Establishing if there ever was life on Mars is fundamental for planning future human missions. -
Dance of the Nomad: a Study of the Selected Notebooks of A.D.Hope
DANCE OF THE NOMAD DANCE OF THE NOMAD A Study of the Selected Notebooks of A. D. Hope ANN McCULLOCH Published by ANU E Press The Australian National University Canberra ACT 0200, Australia Email: [email protected] This title is also available online at: http://epress.anu.edu.au/dance_nomad _citation.html National Library of Australia Cataloguing-in-Publication Entry Author: McCulloch, A. M. (Ann Maree), 1949- Title: Dance of the nomad : a study of the selected notebooks of A.D. Hope / Ann McCulloch. ISBN: 9781921666902 (pbk.) 9781921666919 (eBook) Notes: Includes bibliographical references. Subjects: Hope, A. D. (Alec Derwent), 1907-2000--Criticism and interpretation. Hope, A. D. (Alec Derwent), 1907-2000--Notebooks, sketchbooks, etc. Dewey Number: A828.3 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or trans- mitted in any form or by any means, electronic, mechanical, photocopying or otherwise, without the prior permission of the publisher. Cover design by Emily Brissenden Cover: Professor A. D. Hope. 1991. L. Seselja. NL36907. By permission of National Library of Australia. Printed by Griffin Press This edition © 2010 ANU E Press First edition © 2005 Pandanus Books In memory of my parents Ann and Kevin McDermott and sister in law, Dina McDermott LETTER TO ANN McCULLOCH ‘This may well be rym doggerel’, dear Ann But the best I can manage in liquor so late At night. You asked me where I’d begin in your place. I can Not answer that. But as a general case I might. Drop the proviso, ‘Supposing That I were you’; I find it impossible to think myself in your place But in general almost any writer would do: The problem is much the same in every case. -
Phenotype Inference in an Escherichia Coli Strain Panel
TOOLS AND RESOURCES Phenotype inference in an Escherichia coli strain panel Marco Galardini1, Alexandra Koumoutsi2, Lucia Herrera-Dominguez2, Juan Antonio Cordero Varela1, Anja Telzerow2, Omar Wagih1, Morgane Wartel2, Olivier Clermont3,4, Erick Denamur3,4,5, Athanasios Typas2*, Pedro Beltrao1* 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Hinxton, United Kingdom; 2Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; 3INSERM, IAME, UMR1137, Paris, France; 4Universite´ Paris Diderot, Paris, France; 5APHP, Hoˆpitaux Universitaires Paris Nord Val-de-Seine, Paris, France Abstract Understanding how genetic variation contributes to phenotypic differences is a fundamental question in biology. Combining high-throughput gene function assays with mechanistic models of the impact of genetic variants is a promising alternative to genome-wide association studies. Here we have assembled a large panel of 696 Escherichia coli strains, which we have genotyped and measured their phenotypic profile across 214 growth conditions. We integrated variant effect predictors to derive gene-level probabilities of loss of function for every gene across all strains. Finally, we combined these probabilities with information on conditional gene essentiality in the reference K-12 strain to compute the growth defects of each strain. Not only could we reliably predict these defects in up to 38% of tested conditions, but we could also directly identify the causal variants that were validated through complementation assays. Our work demonstrates the power of forward predictive models and the possibility of precision genetic interventions. DOI: https://doi.org/10.7554/eLife.31035.001 *For correspondence: [email protected] (AT); [email protected] (PB) Introduction Competing interests: The Understanding the genetic and molecular basis of phenotypic differences among individuals is a authors declare that no long-standing problem in biology. -
Molecular Genetics & Genomics
page 46 Lab Times 5-2010 Ranking Illustration: Christina Ullman Publication Analysis 1997-2008 Molecular Genetics & Genomics Under the premise of a “narrow” definition of the field, Germany and England co-dominated European molecular genetics/genomics. The most frequently citated sub-fields were bioinformatical genomics, epigenetics, RNA biology and DNA repair. irst of all, a little science history (you’ll soon see why). As and expression. That’s where so-called computational biology is well known, in the 1950s genetics went molecular – and and systems biology enter research into basic genetic problems. Fdid not just become molecular genetics but rather molec- Given that development, it is not easy to answer the question ular bio logy. In 1963, however, Sydney Brenner wrote in his fa- what “molecular genetics & genomics” today actually is – and, mous letter to Max Perutz: “[...] I have long felt that the future of in particular, what is it in the context of our publication analy- molecular biology lies in the extension of research to other fields sis of the field? It is obvious that, as for example science historian of biology, notably development and the nervous system.” He Robert Olby put it, a “wide” definition can be distinguished from appeared not to be alone with this view and, as a consequence, a “narrow” definition of the field. The wide definition includes along with Brenner many of the leading molecular biologists all fields, into which molecular biology has entered as an exper- from the classical period redirected their research agendas, utilis- imental and theoretical paradigm. The “narrow” definition, on ing the newly developed molecular techniques to investigate un- the other hand, still tries to maintain the status as an explicit bio- solved problems in other fields.