e-Science Research

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Behavioural Virtual Fly Brain Workshop at the University of Oxford, September 2009

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  • The National e-Science Centre coordinates the e-Science effort for the UK. It has a number of activities, one of which is research. This research is interdisciplinary, where Informatics is applied in the context of solving large and complex scientific problems. Such problem solving requires much computational effort and often involves large amounts of data. In this talk I will show the two major components of our research by providing examples of our research projects: 1. To apply Informatics to solve scientific computational problems and 2. to find better ways of organising and facilitating systems that enable these solutions.
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • The development at the MRC has been a spatio-temporal database for developmental biology, this is a basic resource, unique to Edinburgh, for basic and translational research in biomedical science. The key idea is to use a 3D plus time model of embryonic development as a framework for capturing and analysing the genetic activity that controls the developmental process.

    The idea is illustrated here, gene-expression comes in complex patterns through space and time. We need to capture that data and make it available for research. The existing system is based on a design choice made some time ago but is now locked into the system. This leads us to OSAGE. From my perspective this is already a success. I have become locked by a process that required a working database with continuous and all urgent development. The manpower free to re-design and port the underlying database to a new set of standards is zero. eDIKT has made it possible for fresh view of the issues, porting to a future-proofed system based on commercial and emerging Grid/e-Science technlogies. This has already paid off during the analysis phase and the interaction between the eDIKT team and my DB developers. The future will not only benefit the Mouse Atlas but also all the clones and related
  • extrm{similarity}(G_1,G_2) = frac{ extrm{area}(G_1cap G2)}{ extrm{area}(G_1 cup G2)}
  • We need some way of combining gene patterns.
    Pattern can be hand drawn, belong to a specific gene, correspond to anatomical components
  • We need some way of combining gene patterns.
    Pattern can be hand drawn, belong to a specific gene, correspond to anatomical components
  • We need some way of combining gene patterns.
    Pattern can be hand drawn, belong to a specific gene, correspond to anatomical components
  • We need some way of combining gene patterns.
    Pattern can be hand drawn, belong to a specific gene, correspond to anatomical components
  • * Research focuses on progressing computer science
    * by evaluating both generic and tailored methodologies
    * in a multidisciplinary context with
    * rich use cases to test hypotheses
  • e-Science Research

    1. 1. e-Science Research Jano van Hemert NI VER research.nesc.ac.uk U S E IT TH Y O F H G E R D I U N B
    2. 2. Efficient distributed Applied computational systems models Computer Science Interdisciplinary Effective Research Applications Intuitive algorithms interfaces Distributed Collaborative security models environments
    3. 3. Computional Domain Thinkers Specialists Formulation Managing Interaction Data models & Experiments & computational knowledge methods creation Mapping Steering Data-Intensive Engineers Execution Implementations, compute & data resources
    4. 4. Rapid Portal Development Interaction: Steering
    5. 5. GridQTL !
    6. 6. students researcher teacher 2. uses 3. reads 5. performs task 4. deploys portal designer web portal 1 .creates 6. runs jobs XML 7. returns interface, results !"#$%&"'( task & resource description compute resources
    7. 7. Define Compute Resources • Condor / Sun Grid Engine / PBS / GridSAM / Fork process
    8. 8. Next Generation Embryology Interaction: Managing
    9. 9. Current generation 330 source: PhD thesis Marit Boot & EBay
    10. 10. Anatomy is difficult to learn source: Kaufman, Bard, Davidson
    11. 11. How difficult?
    12. 12. first_polar_body mesothelium venous_system cardiac_jelly myocoele vascular_element glossopharyngeal- 4th_arch associated_mesenchym mantle_layer one-cell_stage peritoneal_component anterior_cardinal_vein endocardial_tube sclerotome gland vagus_IX- branchial_groove e marginal_layer second_polar_body cavity primary_head_vein cardiac_muscle somite_16 thyroid_primordium X_preganglion_complex ectoderm primordial_germ_cells ventricular_layer zona_pellucida mesothelium umbilical_vein outflow_tract dermomyotome associated_mesenchym trigeminal_V_preganglio branchial_membrane somite roof_plate two-cell_stage future_midbrain vitelline_vein cardiac_jelly myocoele e n ectoderm somite_31 midbrain How difficult? 4-8_cell_stage floor_plate visceral_organ endocardial_tube sclerotome endoderm vagus_X_preganglion endoderm dermomyotome floor_plate compacted_morula neural_fold alimentary_system mesenchyme somite_17 biliary_bud peripheral_nervous_sys branchial_pouch myocoele lateral_wall embryo neural_crest gut primitive_ventricle dermomyotome extrahepatic_part tem endoderm sclerotome mantle_layer compacted_morula future_prosencephalon foregut_diverticulum cardiac_jelly myocoele intrahepatic_part spinal ectoderm somite_32 marginal_layer inner_cell_mass floor_plate associated_mesenchym endocardial_tube sclerotome epithelium ganglion endoderm dermomyotome ventricular_layer extraembryonic_compo neural_fold e cardiac_muscle somite_18 hepatic_diverticulum dorsal_root_ganglion mesenchyme myocoele mesencephalic_vesicle nent neural_crest endoderm cardinal_vein dermomyotome vascular_element otocyst mesenchyme_derived_f sclerotome roof_plate cavities_and_their_linin future_rhombencephalo hindgut_diverticulum anterior myocoele epithelium associated_mesenchym rom_head_mesoderm somite_33 acoustic_ganglion_VIII gs n associated_mesenchym common sclerotome vascular_element e mesenchyme_derived_f dermomyotome facial_ganglion_VII blastocoelic_cavity anterior_pro- e posterior somite_19 epithelium epithelium rom_neural_crest myocoele autonomic second_polar_body rhombomere endoderm left dermomyotome vascular_element lens_placode pleural_component sclerotome sympathetic trophectoderm floor_plate primordial_germ_cells right myocoele gland mesenchyme cavity somite_34 nerve_trunk mural_trophectoderm neural_fold midgut gland sclerotome pituitary optic_cup mesothelium dermomyotome nerve_plexus polar_trophectoderm neural_crest associated_mesenchym thyroid_primordium somite_20 Rathke's_pouch inner_layer parietal myocoele brachial_plexus zona_pellucida early_hindbrain_neural_ e associated_mesenchym dermomyotome rest_of_ectoderm intraretinal_space visceral sclerotome nerve epiblast ectoderm endoderm e myocoele associated_mesenchym outer_layer apical_ectodermal_ridg somite_35 segmental_spinal_nerv primitive_endoderm floor_plate mouth-foregut_junction foregut-midgut_junction sclerotome e optic_stalk e dermomyotome e endoderm neural_fold buccopharyngeal_mem associated_mesenchym nervous_system nephric_duct naso-lacrimal_groove hindlimb_bud myocoele external_ear parietal_endoderm neural_crest brane e central_nervous_syste primordial_germ_cells process ectoderm sclerotome 1st_branchial_membran cavities posterior_pro- ectoderm mesentery m pronephros fronto-nasal_process mesenchyme neural_crest e yolk_sac_cavity rhombomere endoderm dorsal_mesentery future_brain tail_bud ectoderm ventricular_layer epithelium epithelium intermediate_endoderm floor_plate oral_region urogenital_system future_midbrain branchial_groove mesenchyme ventricular_layer epithelium endolymphatic_append Reichert's_membrane neural_fold stomatodaeum nephric_cord floor_plate ectoderm branchial_arch_artery ventricular_layer cervical_sinus age visceral_endoderm neural_crest mesenchyme presumptive_nephric_d lateral_wall branchial_membrane 1st_arch_artery ventricular_layer greater_sac associated_mesenchym ectoplacental_cone pre-otic_sulcus mesenchyme uct mesencephalic_vesicle ectoderm 2nd_arch_artery ventricular_layer cavity e cavities_and_their_linin neural_fold mesenchyme cardiovascular_system neural_crest endoderm 3rd_arch_artery ventricular_layer mesothelium epithelium gs neural_crest mesenchyme arterial_system roof_plate branchial_pouch atrium ventricular_layer parietal other_part embryonic_component_ neural_tube blood_island umbilical_artery future_rhombencephalo endoderm common_atrial_chambe ventricular_layer omental_bursa associated_mesenchym of_the_proamniotic_cav floor_plate head_mesenchyme common n parietal r ventricular_layer mesothelium e ity lateral_wall mesenchyme_derived_f venous_system 4th_ventricle visceral cardiac_jelly ventricular_layer parietal epithelium endoderm neural_lumen rom_head_mesoderm umbilical_vein rhombomere_01 parietal endocardial_lining ventricular_layer apical_ectodermal_ridg middle_ear primitive_endoderm roof_plate mesenchyme_derived_f common floor_plate parietal cardiac_muscle ventricular_layer e associated_mesenchym extraembryonic_compo mesenchyme_derived_f rom_neural_crest left lateral_wall visceral bulboventricular_groove facio- body-wall_mesenchyme e nent_of_the_proamnioti rom_neural_crest 2nd_arch right roof_plate hindlimb_ridge endocardial_lining acoustic_ganglion_com brain tubo-tympanic_recess c_cavity trigeminal_neural_crest branchial_membrane vitelline_vein rhombomere_02 ectoderm endocardial_lining plex_VII-VIII forebrain surface_ectoderm_of_th ectoderm paraxial_mesenchyme endoderm left floor_plate mesenchyme endocardial_cushion_tis glossopharyngeal_IX diencephalon e_eye primary_trophoblast_gia somite branchial_pouch right lateral_wall lateral_migration_pathw sue glossopharyngeal- gland 4th_arch_artery nt_cells somite_01 endoderm mandibular_component roof_plate ay endocardial_lining vagus_IX- pituitary 6th_arch_artery cytotrophoblast somite_02 ectoderm ectoderm rhombomere_03 medial_migration_path left X_ganglion_complex infundibular_recess_of_ ductus_caroticus syncytiotrophoblast somite_03 endoderm endoderm floor_plate way right trigeminal_V 3rd_ventricle ophthalmic_artery ectoderm somite_04 mesenchyme mesenchyme lateral_wall mesenchyme_derived_f oesophageal_region vagus_X 3rd_ventricle pulmonary_artery definitive_endoderm trunk_mesenchyme mesenchyme_derived_f mesenchyme_derived_f roof_plate rom_somatopleure associated_mesenchym lens_pit diencephalic_part_of_in valve mesoderm intermediate_mesenchy rom_head_mesoderm rom_head_mesoderm rhombomere_04 mesenchyme_derived_f e olfactory_pit terventricular_foramen venous_valve primitive_streak me mesenchyme_derived_f mesenchyme_derived_f floor_plate rom_splanchnopleure epithelium nasal_epithelium optic_recess interatrial_septum neural_ectoderm lateral_plate_mesenchy rom_neural_crest rom_neural_crest lateral_wall somite_21 mesentery frontal_process floor_plate foramen_primum non-neural_ectoderm me pericardio- maxillary_component roof_plate dermomyotome dorsal_meso- ectoderm lamina_terminalis septum_primum node somatopleure peritoneal_canal ectoderm rhombomere_05 myocoele oesophagus mesenchyme lateral_wall ascending_aorta amniotic_fold splanchnopleure cavity endoderm floor_plate sclerotome vascular_element latero-nasal_process mantle_layer pulmonary_trunk ectoderm mesenchyme_derived_f mesothelium mesenchyme lateral_wall somite_22 pharynx ectoderm marginal_layer marginal_vein_of_foreli mesoderm rom_neural_crest roof_plate mesenchyme_derived_f roof_plate dermomyotome associated_mesenchym mesenchyme ventricular_layer mb amniotic_cavity paraxial_mesenchyme hindbrain_posterior_to_ rom_head_mesoderm rhombomere_06 myocoele e medial-nasal_process roof_plate marginal_vein_of_hindli ectoplacental_cavity somite rhombomere_05 mesenchyme_derived_f floor_plate sclerotome epithelium ectoderm telencephalon mb exocoelomic_cavity somite_05 floor_plate rom_neural_crest lateral_wall somite_23 vascular_element mesenchyme mantle_layer principal_vein_of_foreli within_amniotic_fold somite_06 neural_fold maxillary- roof_plate dermomyotome mesentery principal_artery_to_forel marginal_layer mb mesoderm somite_07 neural_crest mandibular_groove rhombomere_07 myocoele dorsal_mesentery imb ventricular_layer principal_vein_of_hindli allantois somite_08 rhombomere_01 ectoderm floor_plate sclerotome ventral_mesentery principal_artery_to_hind lateral_ventricle mb yolk_sac unsegmented_mesench floor_plate branchial_groove lateral_wall somite_24 gall_bladder_primordiu limb telencephalic_part_of_i vitelline_venous_plexus endoderm yme neural_fold ectoderm roof_plate dermomyotome m left_part nterventricular_foramen stomach mesoderm primordial_germ_cells rhombomere_02 ectoderm rhombomere_08 myocoele ventral_mesentery cardiac_jelly hindbrain associated_mesenchym intraembryonic_coelom notochord floor_plate 3rd_arch floor_plate sclerotome hindgut endocardial_lining 4th_ventricle e future_brain sensory_organ neural_fold ectoderm lateral_wall somite_25 associated_mesenchym left_auricular_region rhombomere_01 epithelium neural_fold ear neural_crest endoderm roof_plate dermomyotome e endocardial_lining floor_plate mesentery neural_crest inner_ear rhombomere_03 mesenchyme prosencephalon myocoele epithelium cardiac_muscle lateral_wall dorsal_mesogastrium future_spinal_cord otic_placode floor_plate mesenchyme_derived_f floor_plate sclerotome mesentery cardiac_muscle mantle_layer ventral_mesogastrium neural_fold associated_mesenchym neural_fold rom_head_mesoderm future_diencephalon somite_26 dorsal_mesentery right_part marginal_layer vascular_element neural_crest e neural_crest mesenchyme_derived_f 3rd_ventricle dermomyotome vascular_element cardiac_jelly ventricular_layer postanal_component neural_plate epithelium rhombomere_04 rom_neural_crest floor_plate myocoele mesentery endocardial_lining roof_plate associated_mesenchym surface_ectoderm eye floor_plate limb lateral_wall sclerotome dorsal_mesentery cardiac_muscle rhombomere_02 e mesenchyme optic_sulcus neural_fold forelimb_bud neural_crest somite_27 gland right_auricular_region floor_plate epithelium head_mesenchyme neural_ectoderm neural_crest ectoderm roof_plate dermomyotome pituitary endocardial_lining lateral_wall vascular_element mesenchyme_derived_f arterial_system rhombomere_05 mesenchyme lateral_wall myocoele Rathke's_pouch cardiac_muscle mantle_layer preanal_component rom_head_mesoderm 1st_arch_artery floor_plate lateral_mesenchyme_d prosencephalic_vesicle sclerotome rest_of_ectoderm aortico- marginal_layer associated_mesenchym mesenchyme_derived_f 2nd_arch_artery neural_fold erived_from_mesoderm roof_plate somite_28 respiratory_system pulmonary_spiral_septu ventricular_layer e rom_neural-crest dorsal_aorta neural_crest mesenchyme_derived_f rostral_neuropore dermomyotome lung m roof_plate epithelium notochordal_plate left neural_crest rom_somatopleure neural_crest myocoele left_lung_rudiment inter- rhombomere_03 vascular_element notochordal_process right neural_luminal_occlusio mesenchyme_derived_f future_spinal_cord sclerotome associated_mesenchym subcardinal_venous_an floor_plate loop organ_system vitelline_artery n rom_splanchnopleure caudal_neuropore somite_29 e astomosis lateral_wall associated_mesenchym cardiovascular_system early_primitive_heart_tu facial_neural_crest mesenchyme_derived_f neural_plate dermomyotome epithelium subcardinal_vein mantle_layer e heart be facio- rom_neural_crest neural_fold myocoele vascular_element supracardinal_vein marginal_layer epithelium cardiogenic_plate cardiac_jelly acoustic_neural_crest dermomyotome neural_crest sclerotome right_lung_rudiment anal_region ventricular_layer mesentery allantois endocardial_tube somite_09 myocoele neural_tube somite_30 associated_mesenchym cloacal_membrane roof_plate dorsal_mesentery mesoderm cardiac_muscle somite_10 sclerotome floor_plate dermomyotome e oesophagus rhombomere_04 vascular_element amnion mesentery somite_11 dermomyotome lateral_wall myocoele epithelium associated_mesenchym floor_plate rest_of_midgut ectoderm dorsal_mesocardium somite_12 myocoele neural_lumen sclerotome vascular_element e lateral_wall associated_mesenchym mesoderm transverse_pericardial_ somite_13 sclerotome neural_luminal_occlusio future_forebrain respiratory_tract epithelium mantle_layer e chorion sinus septum_transversum dermomyotome n diencephalon lower mesentery marginal_layer epithelium ectoderm primitive_heart_tube hepatic_component myocoele roof_plate 3rd_ventricle laryngo-tracheal_groove dorsal_meso- ventricular_layer mesentery mesoderm bulbus_cordis non-hepatic_component sclerotome otic_pit diencephalic_part_of_in tracheal_diverticulum oesophagus roof_plate dorsal_mesentery blood_island caudal_half trunk_mesenchyme_fro dermomyotome associated_mesenchym terventricular_foramen associated_mesenchym vascular_element rhombomere_05 vascular_element primordial_germ_cells cardiac_jelly m_neural_crest myocoele e optic_recess e oral_epithelium floor_plate incomplete_urorectal_s branchial_arch endocardial_tube optic_eminence sclerotome epithelium floor_plate epithelium liver_and_biliary_syste lateral_wall eptum 1st_arch cardiac_muscle ectoderm dermomyotome surface_ectoderm gland vascular_element m mantle_layer somite_36 branchial_groove rostral_half mesenchyme myocoele optic_vesicle pituitary mesonephros cystic_duct marginal_layer dermomyotome ectoderm cardiac_jelly optic_pit sclerotome neural_ectoderm infundibular_recess_of_ associated_mesenchym gall_bladder_primordiu ventricular_layer myocoele branchial_membrane endocardial_tube neural_ectoderm dermomyotome nose 3rd_ventricle e m roof_plate sclerotome ectoderm cardiac_muscle common myocoele olfactory_placode lamina_terminalis non-tubular_part hepatic_duct rhombomere_06 somite_37 endoderm common_atrial_chambe internal_carotid_artery sclerotome left lateral_wall tubule extrahepatic_part floor_plate dermomyotome branchial_pouch r left dermomyotome right roof_plate tail intrahepatic_part lateral_wall myocoele endoderm cardiac_jelly right myocoele atrio-ventricular_canal telencephalon mesenchyme liver mantle_layer sclerotome ectoderm endocardial_tube umbilical_artery sclerotome vessels_connecting_int telencephalic_vesicle mesenchyme_derived_f hepatic_primordium marginal_layer somite_38 endoderm cardiac_muscle blood dermomyotome ernal_carotid_artery_to telencephalic_part_of_i rom_neural_crest parenchyma ventricular_layer dermomyotome mesenchyme outflow_tract bulbus_cordis myocoele _primary_head_veins nterventricular_foramen paraxial_mesenchyme main_bronchus roof_plate myocoele mesenchyme_derived_f cardiac_jelly caudal_half sclerotome foregut floor_plate unsegmented_mesench associated_mesenchym rhombomere_07 sclerotome rom_neural_crest endocardial_tube cardiac_jelly dermomyotome pharyngeal_region lateral_wall yme e floor_plate somite_39 mesenchyme_derived_f mesenchyme endocardial_tube myocoele associated_mesenchym roof_plate nervous_system epithelium lateral_wall dermomyotome rom_head_mesoderm primitive_ventricle cardiac_muscle sclerotome e ganglion central_nervous_syste vascular_element mantle_layer myocoele pericardial_component cardiac_jelly rostral_half somite_14 epithelium cranial m trachea marginal_layer sclerotome cavity endocardial_tube cardiac_jelly dermomyotome vascular_element facio-acoustic_VII- future_spinal_cord associated_mesenchym ventricular_layer gland mesothelium cardiac_muscle endocardial_tube myocoele rest_of_foregut VIII_preganglion_compl neural_plate e roof_plate pancreas_primordium pericardio- sinus_venosus cardiac_muscle sclerotome associated_mesenchym ex neural_tube epithelium rhombomere_08 dorsal_bud peritoneal_component left_horn common_atrial_chambe somite_15 e glossopharyngeal_IX_pr dorsal vascular_element floor_plate thyroid cavity right_horn r dermomyotome epithelium eganglion ventral gonadal_component lateral_wall foramen_caecum
    13. 13. first_polar_body mesothelium venous_system cardiac_jelly myocoele vascular_element glossopharyngeal- 4th_arch associated_mesenchym mantle_layer one-cell_stage peritoneal_component anterior_cardinal_vein endocardial_tube sclerotome gland vagus_IX- branchial_groove e marginal_layer second_polar_body cavity primary_head_vein cardiac_muscle somite_16 thyroid_primordium X_preganglion_complex ectoderm primordial_germ_cells ventricular_layer zona_pellucida mesothelium umbilical_vein outflow_tract dermomyotome associated_mesenchym trigeminal_V_preganglio branchial_membrane somite roof_plate two-cell_stage future_midbrain vitelline_vein cardiac_jelly myocoele e n ectoderm somite_31 midbrain How difficult? 4-8_cell_stage floor_plate visceral_organ endocardial_tube sclerotome endoderm vagus_X_preganglion endoderm dermomyotome floor_plate compacted_morula neural_fold alimentary_system mesenchyme somite_17 biliary_bud peripheral_nervous_sys branchial_pouch myocoele lateral_wall embryo neural_crest gut primitive_ventricle dermomyotome extrahepatic_part tem endoderm sclerotome mantle_layer compacted_morula future_prosencephalon foregut_diverticulum cardiac_jelly myocoele intrahepatic_part spinal ectoderm somite_32 marginal_layer inner_cell_mass floor_plate associated_mesenchym endocardial_tube sclerotome epithelium ganglion endoderm dermomyotome ventricular_layer extraembryonic_compo neural_fold e cardiac_muscle somite_18 hepatic_diverticulum dorsal_root_ganglion mesenchyme myocoele mesencephalic_vesicle nent neural_crest endoderm cardinal_vein dermomyotome vascular_element otocyst mesenchyme_derived_f sclerotome roof_plate cavities_and_their_linin future_rhombencephalo hindgut_diverticulum anterior myocoele epithelium associated_mesenchym rom_head_mesoderm somite_33 acoustic_ganglion_VIII gs n associated_mesenchym common sclerotome vascular_element e mesenchyme_derived_f dermomyotome facial_ganglion_VII blastocoelic_cavity anterior_pro- e posterior somite_19 epithelium epithelium rom_neural_crest myocoele autonomic second_polar_body rhombomere endoderm left dermomyotome vascular_element lens_placode pleural_component sclerotome sympathetic trophectoderm floor_plate primordial_germ_cells right myocoele gland mesenchyme cavity somite_34 nerve_trunk mural_trophectoderm neural_fold midgut gland sclerotome pituitary optic_cup mesothelium dermomyotome nerve_plexus polar_trophectoderm neural_crest associated_mesenchym thyroid_primordium somite_20 Rathke's_pouch inner_layer parietal myocoele brachial_plexus zona_pellucida early_hindbrain_neural_ e associated_mesenchym dermomyotome rest_of_ectoderm intraretinal_space visceral sclerotome nerve epiblast ectoderm endoderm e myocoele associated_mesenchym outer_layer apical_ectodermal_ridg somite_35 segmental_spinal_nerv primitive_endoderm floor_plate mouth-foregut_junction foregut-midgut_junction sclerotome e optic_stalk e dermomyotome e endoderm neural_fold buccopharyngeal_mem associated_mesenchym nervous_system nephric_duct naso-lacrimal_groove hindlimb_bud myocoele external_ear parietal_endoderm neural_crest brane e central_nervous_syste primordial_germ_cells process ectoderm sclerotome 1st_branchial_membran cavities posterior_pro- ectoderm mesentery m pronephros fronto-nasal_process mesenchyme neural_crest e yolk_sac_cavity rhombomere endoderm dorsal_mesentery future_brain tail_bud ectoderm ventricular_layer epithelium epithelium intermediate_endoderm floor_plate oral_region urogenital_system future_midbrain branchial_groove mesenchyme ventricular_layer epithelium endolymphatic_append Reichert's_membrane neural_fold stomatodaeum nephric_cord floor_plate ectoderm branchial_arch_artery ventricular_layer cervical_sinus age visceral_endoderm neural_crest mesenchyme presumptive_nephric_d lateral_wall branchial_membrane 1st_arch_artery ventricular_layer greater_sac associated_mesenchym ectoplacental_cone pre-otic_sulcus mesenchyme uct mesencephalic_vesicle ectoderm 2nd_arch_artery ventricular_layer cavity e cavities_and_their_linin neural_fold mesenchyme cardiovascular_system neural_crest endoderm 3rd_arch_artery ventricular_layer mesothelium epithelium gs neural_crest mesenchyme arterial_system roof_plate branchial_pouch atrium ventricular_layer parietal other_part embryonic_component_ neural_tube blood_island umbilical_artery future_rhombencephalo endoderm common_atrial_chambe ventricular_layer omental_bursa associated_mesenchym of_the_proamniotic_cav floor_plate head_mesenchyme common n parietal r ventricular_layer mesothelium e ity lateral_wall mesenchyme_derived_f venous_system 4th_ventricle visceral cardiac_jelly ventricular_layer parietal epithelium endoderm neural_lumen rom_head_mesoderm umbilical_vein rhombomere_01 parietal endocardial_lining ventricular_layer apical_ectodermal_ridg middle_ear primitive_endoderm roof_plate mesenchyme_derived_f common floor_plate parietal cardiac_muscle ventricular_layer e associated_mesenchym extraembryonic_compo mesenchyme_derived_f rom_neural_crest left lateral_wall visceral bulboventricular_groove facio- body-wall_mesenchyme e nent_of_the_proamnioti rom_neural_crest 2nd_arch right roof_plate hindlimb_ridge endocardial_lining acoustic_ganglion_com brain tubo-tympanic_recess c_cavity trigeminal_neural_crest branchial_membrane vitelline_vein rhombomere_02 ectoderm endocardial_lining plex_VII-VIII forebrain surface_ectoderm_of_th ectoderm paraxial_mesenchyme endoderm left floor_plate mesenchyme endocardial_cushion_tis glossopharyngeal_IX diencephalon e_eye primary_trophoblast_gia somite branchial_pouch right lateral_wall lateral_migration_pathw sue glossopharyngeal- gland 4th_arch_artery nt_cells somite_01 endoderm mandibular_component roof_plate ay endocardial_lining vagus_IX- pituitary 6th_arch_artery cytotrophoblast somite_02 ectoderm ectoderm rhombomere_03 medial_migration_path left X_ganglion_complex infundibular_recess_of_ ductus_caroticus syncytiotrophoblast somite_03 endoderm endoderm floor_plate way right trigeminal_V 3rd_ventricle ophthalmic_artery ectoderm somite_04 mesenchyme mesenchyme lateral_wall mesenchyme_derived_f oesophageal_region vagus_X 3rd_ventricle pulmonary_artery definitive_endoderm trunk_mesenchyme mesenchyme_derived_f mesenchyme_derived_f roof_plate rom_somatopleure associated_mesenchym lens_pit diencephalic_part_of_in valve mesoderm intermediate_mesenchy rom_head_mesoderm rom_head_mesoderm rhombomere_04 mesenchyme_derived_f e olfactory_pit terventricular_foramen venous_valve primitive_streak me mesenchyme_derived_f mesenchyme_derived_f floor_plate rom_splanchnopleure epithelium nasal_epithelium optic_recess interatrial_septum neural_ectoderm lateral_plate_mesenchy rom_neural_crest rom_neural_crest lateral_wall somite_21 mesentery frontal_process floor_plate foramen_primum non-neural_ectoderm me pericardio- maxillary_component roof_plate dermomyotome dorsal_meso- ectoderm lamina_terminalis septum_primum node somatopleure peritoneal_canal ectoderm rhombomere_05 myocoele oesophagus mesenchyme lateral_wall ascending_aorta amniotic_fold splanchnopleure cavity endoderm floor_plate sclerotome vascular_element latero-nasal_process mantle_layer pulmonary_trunk ectoderm mesenchyme_derived_f mesothelium mesenchyme lateral_wall somite_22 pharynx ectoderm marginal_layer marginal_vein_of_foreli mesoderm rom_neural_crest roof_plate mesenchyme_derived_f roof_plate dermomyotome associated_mesenchym mesenchyme ventricular_layer mb amniotic_cavity paraxial_mesenchyme hindbrain_posterior_to_ rom_head_mesoderm rhombomere_06 myocoele e medial-nasal_process roof_plate marginal_vein_of_hindli ectoplacental_cavity somite rhombomere_05 mesenchyme_derived_f floor_plate sclerotome epithelium ectoderm telencephalon mb exocoelomic_cavity somite_05 floor_plate rom_neural_crest lateral_wall somite_23 vascular_element mesenchyme mantle_layer principal_vein_of_foreli within_amniotic_fold somite_06 neural_fold maxillary- roof_plate dermomyotome mesentery principal_artery_to_forel marginal_layer mb mesoderm somite_07 neural_crest mandibular_groove rhombomere_07 myocoele dorsal_mesentery imb ventricular_layer principal_vein_of_hindli allantois somite_08 rhombomere_01 ectoderm floor_plate sclerotome ventral_mesentery principal_artery_to_hind lateral_ventricle mb mesenchyme derived yolk_sac unsegmented_mesench floor_plate branchial_groove lateral_wall somite_24 gall_bladder_primordiu limb telencephalic_part_of_i vitelline_venous_plexus endoderm yme neural_fold ectoderm roof_plate dermomyotome m left_part nterventricular_foramen stomach mesoderm primordial_germ_cells rhombomere_02 ectoderm rhombomere_08 myocoele ventral_mesentery cardiac_jelly hindbrain associated_mesenchym intraembryonic_coelom notochord floor_plate 3rd_arch floor_plate sclerotome hindgut endocardial_lining 4th_ventricle e future_brain sensory_organ neural_fold ectoderm lateral_wall somite_25 associated_mesenchym left_auricular_region rhombomere_01 epithelium neural_fold ear neural_crest endoderm roof_plate dermomyotome e endocardial_lining floor_plate mesentery neural_crest inner_ear rhombomere_03 mesenchyme prosencephalon myocoele epithelium cardiac_muscle lateral_wall dorsal_mesogastrium future_spinal_cord otic_placode floor_plate mesenchyme_derived_f floor_plate sclerotome mesentery cardiac_muscle mantle_layer ventral_mesogastrium neural_fold associated_mesenchym neural_fold rom_head_mesoderm future_diencephalon somite_26 dorsal_mesentery right_part marginal_layer vascular_element from splanchnopleure neural_crest e neural_crest mesenchyme_derived_f 3rd_ventricle dermomyotome vascular_element cardiac_jelly ventricular_layer postanal_component neural_plate epithelium rhombomere_04 rom_neural_crest floor_plate myocoele mesentery endocardial_lining roof_plate associated_mesenchym surface_ectoderm eye floor_plate limb lateral_wall sclerotome dorsal_mesentery cardiac_muscle rhombomere_02 e mesenchyme optic_sulcus neural_fold forelimb_bud neural_crest somite_27 gland right_auricular_region floor_plate epithelium head_mesenchyme neural_ectoderm neural_crest ectoderm roof_plate dermomyotome pituitary endocardial_lining lateral_wall vascular_element mesenchyme_derived_f arterial_system rhombomere_05 mesenchyme lateral_wall myocoele Rathke's_pouch cardiac_muscle mantle_layer preanal_component rom_head_mesoderm 1st_arch_artery floor_plate lateral_mesenchyme_d prosencephalic_vesicle sclerotome rest_of_ectoderm aortico- marginal_layer associated_mesenchym mesenchyme_derived_f 2nd_arch_artery neural_fold erived_from_mesoderm roof_plate somite_28 respiratory_system pulmonary_spiral_septu ventricular_layer e rom_neural-crest dorsal_aorta neural_crest mesenchyme_derived_f rostral_neuropore dermomyotome lung m roof_plate epithelium notochordal_plate left neural_crest rom_somatopleure neural_crest myocoele left_lung_rudiment inter- rhombomere_03 vascular_element notochordal_process right neural_luminal_occlusio mesenchyme_derived_f future_spinal_cord sclerotome associated_mesenchym subcardinal_venous_an floor_plate loop organ_system vitelline_artery n rom_splanchnopleure caudal_neuropore somite_29 e astomosis lateral_wall associated_mesenchym cardiovascular_system early_primitive_heart_tu facial_neural_crest mesenchyme_derived_f neural_plate dermomyotome epithelium subcardinal_vein mantle_layer e heart be facio- rom_neural_crest neural_fold myocoele vascular_element supracardinal_vein marginal_layer epithelium cardiogenic_plate cardiac_jelly acoustic_neural_crest dermomyotome neural_crest sclerotome right_lung_rudiment anal_region ventricular_layer mesentery allantois endocardial_tube somite_09 myocoele neural_tube somite_30 associated_mesenchym cloacal_membrane roof_plate dorsal_mesentery mesoderm cardiac_muscle somite_10 sclerotome floor_plate dermomyotome e oesophagus rhombomere_04 vascular_element amnion mesentery somite_11 dermomyotome lateral_wall myocoele epithelium associated_mesenchym floor_plate rest_of_midgut ectoderm dorsal_mesocardium somite_12 myocoele neural_lumen sclerotome vascular_element e lateral_wall associated_mesenchym mesoderm transverse_pericardial_ somite_13 sclerotome neural_luminal_occlusio future_forebrain respiratory_tract epithelium mantle_layer e chorion sinus septum_transversum dermomyotome n diencephalon lower mesentery marginal_layer epithelium ectoderm primitive_heart_tube hepatic_component myocoele roof_plate 3rd_ventricle laryngo-tracheal_groove dorsal_meso- ventricular_layer mesentery mesoderm bulbus_cordis non-hepatic_component sclerotome otic_pit diencephalic_part_of_in tracheal_diverticulum oesophagus roof_plate dorsal_mesentery blood_island caudal_half trunk_mesenchyme_fro dermomyotome associated_mesenchym terventricular_foramen associated_mesenchym vascular_element rhombomere_05 vascular_element primordial_germ_cells cardiac_jelly m_neural_crest myocoele e optic_recess e oral_epithelium floor_plate incomplete_urorectal_s branchial_arch endocardial_tube optic_eminence sclerotome epithelium floor_plate epithelium liver_and_biliary_syste lateral_wall eptum 1st_arch cardiac_muscle ectoderm dermomyotome surface_ectoderm gland vascular_element m mantle_layer somite_36 branchial_groove rostral_half mesenchyme myocoele optic_vesicle pituitary mesonephros cystic_duct marginal_layer dermomyotome ectoderm cardiac_jelly optic_pit sclerotome neural_ectoderm infundibular_recess_of_ associated_mesenchym gall_bladder_primordiu ventricular_layer myocoele branchial_membrane endocardial_tube neural_ectoderm dermomyotome nose 3rd_ventricle e m roof_plate sclerotome ectoderm cardiac_muscle common myocoele olfactory_placode lamina_terminalis non-tubular_part hepatic_duct rhombomere_06 somite_37 endoderm common_atrial_chambe internal_carotid_artery sclerotome left lateral_wall tubule extrahepatic_part floor_plate dermomyotome branchial_pouch r left dermomyotome right roof_plate tail intrahepatic_part lateral_wall myocoele endoderm cardiac_jelly right myocoele atrio-ventricular_canal telencephalon mesenchyme liver mantle_layer sclerotome ectoderm endocardial_tube umbilical_artery sclerotome vessels_connecting_int telencephalic_vesicle mesenchyme_derived_f hepatic_primordium marginal_layer somite_38 endoderm cardiac_muscle blood dermomyotome ernal_carotid_artery_to telencephalic_part_of_i rom_neural_crest parenchyma ventricular_layer dermomyotome mesenchyme outflow_tract bulbus_cordis myocoele _primary_head_veins nterventricular_foramen paraxial_mesenchyme main_bronchus roof_plate myocoele mesenchyme_derived_f cardiac_jelly caudal_half sclerotome foregut floor_plate unsegmented_mesench associated_mesenchym rhombomere_07 sclerotome rom_neural_crest endocardial_tube cardiac_jelly dermomyotome pharyngeal_region lateral_wall yme e floor_plate somite_39 mesenchyme_derived_f mesenchyme endocardial_tube myocoele associated_mesenchym roof_plate nervous_system epithelium lateral_wall dermomyotome rom_head_mesoderm primitive_ventricle cardiac_muscle sclerotome e ganglion central_nervous_syste vascular_element mantle_layer myocoele pericardial_component cardiac_jelly rostral_half somite_14 epithelium cranial m trachea marginal_layer sclerotome cavity endocardial_tube cardiac_jelly dermomyotome vascular_element facio-acoustic_VII- future_spinal_cord associated_mesenchym ventricular_layer gland mesothelium cardiac_muscle endocardial_tube myocoele rest_of_foregut VIII_preganglion_compl neural_plate e roof_plate pancreas_primordium pericardio- sinus_venosus cardiac_muscle sclerotome associated_mesenchym ex neural_tube epithelium rhombomere_08 dorsal_bud peritoneal_component left_horn common_atrial_chambe somite_15 e glossopharyngeal_IX_pr dorsal vascular_element floor_plate thyroid cavity right_horn r dermomyotome epithelium eganglion ventral gonadal_component lateral_wall foramen_caecum
    14. 14. Spatial learning Space and Anatomy source: Richard Baldock, MRC HGU
    15. 15. Mapping gene expression source: Mark Scott, Newcastle University
    16. 16. Mapping gene expression source: Mark Scott, Newcastle University
    17. 17. 3D maps source: Richard Baldock, MRC HGU
    18. 18. 3D maps Annotate source: Richard Baldock, MRC HGU
    19. 19. Learning by space source: Richard Baldock, MRC HGU
    20. 20. Learning by space source: Richard Baldock, MRC HGU
    21. 21. Learning by space source: Richard Baldock, MRC HGU
    22. 22. Web 2.0
    23. 23. Next generation technology Current Repository Enhanced Repository Query, Navigation & Contribution Query & Contribution Navigation Web & Java clients e-MouseAtlas e-MouseAtlas+ Web clients DSpace + webviewer Knowledge + Maps Knowledge Maps
    24. 24. Data Mining Formulation
    25. 25. Similarity between two gene expression patterns G1 ∩ G2 area(G1 ∩ G2) similarity(G1 , G2 ) = area(G1 ∪ G2) G1 G2 G1 ∪ G2
    26. 26. Similarity between two gene expression patterns G1 ∩ G2 area(G1 ∩ G2) similarity(G1 , G2 ) = area(G1 ∪ G2) G1 G2 G1 ∪ G2 similarity ( , ) = 0.41
    27. 27. Hierarchical clustering ‘Gray’ Data
    28. 28. Hierarchical clustering Lihao Liang (e-Science MSc)
    29. 29. ? What combination of genes defines a given expression pattern?
    30. 30. ? What combination of genes defines a given expression pattern?
    31. 31. ? What combination of genes defines a given expression pattern? gene z gene y gene x
    32. 32. Association Rules Mining Lhx4, Otx2 => Dmbx1
    33. 33. Association Rules Mining Support 0.065 Confidence 0.971 Lift 10.871 Lhx4, Otx2 => Dmbx1
    34. 34. Association Rules Mining Support 0.065 Confidence 0.971 Lift 10.871 Lhx4, Otx2 => Dmbx1 Lhx4 Otx2 Dmbx1
    35. 35. Interaction trees 0.8 average quality 0.7 best quality 0.6 0.5 Similarity 0.4 0.3 0.2 0.1 0 0 200 400 600 800 1000 1200 1400 Evaluations
    36. 36.                                                
    37. 37. Chemistry Gene Therapy in Cystic Fibrosis Developmental Emergency Quantitative Biology Response Genetics Flood Prediction Fly Brain Brain Imaging
    38. 38. Team & Acknowledgements Research Assistants School of Informatics, University of EaStCHEM Patricia Richardson King’s College London Szegedi Tobias Blanke Tudományegyete Jos Koetsier Edinburgh Douglas Armstrong Carole Morrison Neil Robertson Mark Hedges m István Juhos Liangxiu Han Dave Robertson Alan Bundy Sharon Ashbrook University of Manchester University of Minnesota David Rodriguez Stuart Aitken Austin Tate OMII-UK Neil Chue Hong Carole Goble Stian Søiland Jon Weissman Gagarine Yaikhom EPCC Simon Hettrick European Technische Universität Wien Laura Valkonen Andy Turner Rob Baxter Human Genetics Unit, Medical Research Mediterranean Seismological Günther Raidl Martin Grüber Mark Parsons Council Centre Radek Ostrowski Richard Baldock Rémy Bossu Universität Wien PhD Students Ally Hume Amy Krause Jeff Christiansen Bill Hill Peter Brezany Heriot-Watt University Alexander Wöhrer Thomas French Jon Hill Terry Sloan Guangjie Feng Albert Burger Ivan Janciak Ibrahim Elsayed Luna De Ferrari School of GeoSciences Institute of Human Genetics, KNMI, The Netherlands Sabri Pllana Torild van Eck Ehtesham ul Haq Dar Rob Kitchen Rachel Walcott Newcastle University Universidad Politécnica Fakhri Alam Khan Chee-Sun Liew Molecular Medicine Centre Susan Lindsay Steven Lisgo de Madrid Oscar Corcho University Tübingen Sandra Gesing Fan Zhu David Porteous Varrie Ogilvie Xunxian Wang Carlos Buil Miguel Esteban Gutierrez Ustav informatiky, University of Oxford Asuncion Gomez-Perez Slovenskej Research Students Division of Psychiatry Adam Barker Stephen Lawrie Akadémie Vied Universidad de Málaga Ladislav Hluchý Gary Dominic Job Fujitsy Laboratories Europe Carlos Cotta Ondrej Habala Branislav Simo SFC Brain Imaging David Snelling Université Libre de Marek Ciglan Research Centre Sven van den Berghe Bruxelles Michal Laclavik Joanna Wardlaw Vivian Li Tom Lenaerts Emil Gatial Trevor Carpenter Viet Tran http://research.nesc.ac.uk/ Jano van Hemert

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