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Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757.","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757."},"date_updated":"2024-02-21T13:59:18Z","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"}],"article_processing_charge":"No","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","file_date_updated":"2020-07-14T12:47:11Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology 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Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:108","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108","mla":"Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:108.","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, 10.15479/AT:ISTA:108.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:108."},"title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:07Z","author":[{"id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia","full_name":"Igler, Claudia","last_name":"Igler"},{"full_name":"Lagator, Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"article_processing_charge":"No"},{"file":[{"file_size":1336936,"date_updated":"2020-07-14T12:47:03Z","creator":"system","file_name":"IST-2017-61-v1+1_bint_fishmovie32_100.mat","date_created":"2018-12-12T13:03:04Z","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access","checksum":"e620eff260646f57b479a69492c8b765","file_id":"5622"},{"access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5623","checksum":"de83f9b81ea0aae3cddfc3ed982e0759","creator":"system","date_updated":"2020-07-14T12:47:03Z","file_size":1897543,"date_created":"2018-12-12T13:03:05Z","file_name":"IST-2017-61-v1+2_bint_fishmovie32_100.zip"}],"day":"27","year":"2017","datarep_id":"61","has_accepted_license":"1","date_created":"2018-12-12T12:31:33Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"2257"}]},"doi":"10.15479/AT:ISTA:61","date_published":"2017-02-27T00:00:00Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408."}],"month":"02","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:61.","ista":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode array recording from salamander retinal ganglion cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:61.","mla":"Marre, Olivier, et al. Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:61.","ieee":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode array recording from salamander retinal ganglion cells.” Institute of Science and Technology Austria, 2017.","short":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017).","ama":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode array recording from salamander retinal ganglion cells. 2017. doi:10.15479/AT:ISTA:61","apa":"Marre, O., Tkačik, G., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2017). Multi-electrode array recording from salamander retinal ganglion cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:61"},"date_updated":"2024-02-21T13:46:14Z","department":[{"_id":"GaTk"}],"title":"Multi-electrode array recording from salamander retinal ganglion cells","file_date_updated":"2020-07-14T12:47:03Z","article_processing_charge":"No","author":[{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"last_name":"Amodei","full_name":"Amodei, Dario","first_name":"Dario"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"},{"first_name":"Michael","full_name":"Berry, Michael","last_name":"Berry"}],"_id":"5562","keyword":["multi-electrode recording","retinal ganglion cells"],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"citation":{"ista":"Kainmueller D, Jug F, Rother C, Meyers G. 2017. Graph matching problems for annotating C. Elegans, Institute of Science and Technology Austria, 10.15479/AT:ISTA:57.","chicago":"Kainmueller, Dagmar, Florian Jug, Carsten Rother, and Gene Meyers. “Graph Matching Problems for Annotating C. Elegans.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:57.","short":"D. Kainmueller, F. Jug, C. Rother, G. Meyers, (2017).","ieee":"D. Kainmueller, F. Jug, C. Rother, and G. Meyers, “Graph matching problems for annotating C. Elegans.” Institute of Science and Technology Austria, 2017.","ama":"Kainmueller D, Jug F, Rother C, Meyers G. Graph matching problems for annotating C. Elegans. 2017. doi:10.15479/AT:ISTA:57","apa":"Kainmueller, D., Jug, F., Rother, C., & Meyers, G. (2017). Graph matching problems for annotating C. Elegans. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:57","mla":"Kainmueller, Dagmar, et al. Graph Matching Problems for Annotating C. Elegans. 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Elegans.\" by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in \"Feature Correspondence via Graph Matching: Models and Global Optimization.\" by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. ","lang":"eng"}],"month":"02","oa":1,"publisher":"Institute of Science and Technology Austria"},{"file_date_updated":"2020-07-14T12:47:03Z","title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","department":[{"_id":"ToBo"}],"article_processing_charge":"No","author":[{"orcid":"0000-0001-6549-4177","full_name":"Lukacisin, Martin","last_name":"Lukacisin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["571"],"date_updated":"2024-02-21T13:46:47Z","citation":{"ieee":"M. Lukacisin, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2017.","short":"M. Lukacisin, (2017).","apa":"Lukacisin, M. (2017). 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Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. \r\nThe Video is licensed under a CC BY NC ND license. 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We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)","lang":"eng"}],"oa_version":"Published Version"},{"status":"public","keyword":["cell migration","wide field microscopy","FIJI"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"5555","title":"Fiji script to determine average speed and direction of migration of cells","file_date_updated":"2020-07-14T12:47:02Z","department":[{"_id":"Bio"}],"author":[{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2024-02-21T13:50:06Z","citation":{"chicago":"Hauschild, Robert. “Fiji Script to Determine Average Speed and Direction of Migration of Cells.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:44.","ista":"Hauschild R. 2016. Fiji script to determine average speed and direction of migration of cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:44.","mla":"Hauschild, Robert. Fiji Script to Determine Average Speed and Direction of Migration of Cells. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:44.","apa":"Hauschild, R. (2016). Fiji script to determine average speed and direction of migration of cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:44","ama":"Hauschild R. Fiji script to determine average speed and direction of migration of cells. 2016. doi:10.15479/AT:ISTA:44","short":"R. Hauschild, (2016).","ieee":"R. Hauschild, “Fiji script to determine average speed and direction of migration of cells.” Institute of Science and Technology Austria, 2016."},"month":"07","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"text":"This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.","lang":"eng"}],"doi":"10.15479/AT:ISTA:44","date_published":"2016-07-08T00:00:00Z","date_created":"2018-12-12T12:31:31Z","file":[{"date_created":"2018-12-12T13:03:03Z","file_name":"IST-2016-44-v1+1_migrationAnalyzer.zip","creator":"system","date_updated":"2020-07-14T12:47:02Z","file_size":20692,"checksum":"9f96cddbcd4ed689f48712ffe234d5e5","file_id":"5621","access_level":"open_access","relation":"main_file","content_type":"application/zip"}],"day":"08","has_accepted_license":"1","year":"2016","datarep_id":"44"},{"keyword":["discrete tomography"],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","_id":"5557","department":[{"_id":"VlKo"}],"title":"Synthetic discrete tomography problems","file_date_updated":"2020-07-14T12:47:02Z","article_processing_charge":"No","author":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","full_name":"Swoboda, Paul","last_name":"Swoboda"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["006"],"citation":{"ista":"Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science and Technology Austria, 10.15479/AT:ISTA:46.","chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:46.","ama":"Swoboda P. Synthetic discrete tomography problems. 2016. doi:10.15479/AT:ISTA:46","apa":"Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:46","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016.","short":"P. Swoboda, (2016).","mla":"Swoboda, Paul. Synthetic Discrete Tomography Problems. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:46."},"date_updated":"2024-02-21T13:50:21Z","month":"09","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and 256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5."}],"date_created":"2018-12-12T12:31:31Z","contributor":[{"last_name":"Kuske","first_name":"Jan","contributor_type":"data_collector"}],"doi":"10.15479/AT:ISTA:46","date_published":"2016-09-20T00:00:00Z","day":"20","file":[{"date_created":"2018-12-12T13:05:19Z","file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip","date_updated":"2020-07-14T12:47:02Z","file_size":36058401,"creator":"system","checksum":"aa5a16a0dc888da7186fb8fc45e88439","file_id":"5645","content_type":"application/zip","access_level":"open_access","relation":"main_file"}],"year":"2016","datarep_id":"46","has_accepted_license":"1"},{"status":"public","keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"5553","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","file_date_updated":"2020-07-14T12:47:01Z","department":[{"_id":"NiBa"}],"author":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field"},{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis"}],"article_processing_charge":"No","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, 10.15479/AT:ISTA:37.","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:37.","short":"D. Field, T. Ellis, (2016).","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","apa":"Field, D., & Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:37","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37","mla":"Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:37."},"date_updated":"2024-02-21T13:51:14Z","month":"02","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org."}],"date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:37","related_material":{"record":[{"status":"public","id":"1398","relation":"research_paper"}]},"date_created":"2018-12-12T12:31:30Z","contributor":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","contributor_type":"project_manager","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:47:01Z","file_size":132808,"date_created":"2018-12-12T13:03:02Z","file_name":"IST-2016-37-v1+1_paternity_archive.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","checksum":"4ae751b1fa4897fa216241f975a57313","file_id":"5620"}],"day":"19","has_accepted_license":"1","year":"2016","datarep_id":"37"},{"has_accepted_license":"1","year":"2016","datarep_id":"35","file":[{"file_id":"5640","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2018-12-12T13:05:12Z","file_name":"IST-2016-35-v1+1_array_data.zip","creator":"system","date_updated":"2020-07-14T12:47:01Z","file_size":32775}],"day":"19","doi":"10.15479/AT:ISTA:35","date_published":"2016-02-19T00:00:00Z","related_material":{"record":[{"status":"public","id":"1398","relation":"research_paper"}]},"date_created":"2018-12-12T12:31:29Z","contributor":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","citation":{"ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:35.","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35.","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35","short":"T. Ellis, (2016).","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","mla":"Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35."},"date_updated":"2024-02-21T13:51:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:01Z","department":[{"_id":"NiBa"}],"title":"Data on pollinator observations and offpsring phenotypes","_id":"5551","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation."}],"month":"02","publisher":"Institute of Science and Technology Austria","oa":1,"day":"19","file":[{"file_id":"5625","checksum":"cbc61b523d4d475a04a737d50dc470ef","content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T13:03:07Z","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","date_updated":"2020-07-14T12:47:01Z","file_size":44905,"creator":"system"}],"has_accepted_license":"1","year":"2016","datarep_id":"36","date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:36","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1398"}]},"date_created":"2018-12-12T12:31:30Z","contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"_id":"5552","status":"public","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:36","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","short":"T. Ellis, (2016).","mla":"Ellis, Thomas. Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:36.","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, 10.15479/AT:ISTA:36.","chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:36."},"date_updated":"2024-02-21T13:51:40Z","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","file_date_updated":"2020-07-14T12:47:01Z","department":[{"_id":"NiBa"}],"author":[{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No"},{"status":"public","keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"5554","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","file_date_updated":"2020-07-14T12:47:01Z","author":[{"last_name":"Tugrul","orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:50:34Z","citation":{"apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:10.15479/AT:ISTA:43","short":"M. Tugrul, (2016).","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","mla":"Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43.","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43.","chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43."},"month":"05","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution."}],"doi":"10.15479/AT:ISTA:43","date_published":"2016-05-12T00:00:00Z","related_material":{"record":[{"id":"1131","status":"public","relation":"used_in_publication"}]},"contributor":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Magdalena","last_name":"Steinrück"},{"id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","first_name":"Fabienne","contributor_type":"researcher","last_name":"Jesse"}],"date_created":"2018-12-12T12:31:30Z","day":"12","file":[{"file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","date_created":"2018-12-12T13:03:08Z","file_size":1123495,"date_updated":"2020-07-14T12:47:01Z","creator":"system","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","file_id":"5626","content_type":"application/zip","relation":"main_file","access_level":"open_access"}],"has_accepted_license":"1","datarep_id":"43","year":"2016"},{"abstract":[{"text":"PhD thesis LaTeX source code","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"09","has_accepted_license":"1","datarep_id":"48","year":"2016","day":"23","file":[{"date_updated":"2020-07-14T12:47:02Z","file_size":55237885,"creator":"system","date_created":"2018-12-12T13:02:18Z","file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2","content_type":"application/x-bzip2","access_level":"open_access","relation":"main_file","checksum":"5b1b256ad796fbddb4b7729f5e45e444","file_id":"5589"}],"related_material":{"record":[{"relation":"other","id":"1122","status":"public"}]},"doi":"10.15479/AT:ISTA:48","date_published":"2016-09-23T00:00:00Z","date_created":"2018-12-12T12:31:31Z","_id":"5558","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"640","citation":{"mla":"Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:48.","apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:48","ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:10.15479/AT:ISTA:48","short":"M. Bojsen-Hansen, (2016).","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016.","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:48.","ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 10.15479/AT:ISTA:48."},"date_updated":"2024-02-21T13:50:48Z","ddc":["004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224","last_name":"Bojsen-Hansen"}],"publist_id":"6238","article_processing_charge":"No","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:47:02Z","title":"Tracking, Correcting and Absorbing Water Surface Waves"},{"date_created":"2018-12-12T12:31:31Z","date_published":"2016-08-25T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"8431","status":"deleted"},{"status":"public","id":"1029","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:45","year":"2016","datarep_id":"45","has_accepted_license":"1","day":"25","file":[{"file_name":"IST-2016-45-v1+1_PaperCode.zip","date_created":"2018-12-12T13:02:58Z","file_size":296722548,"date_updated":"2020-07-14T12:47:02Z","creator":"system","file_id":"5616","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","content_type":"application/zip","relation":"main_file","access_level":"open_access"}],"oa":1,"publisher":"Institute of Science and Technology Austria","month":"08","abstract":[{"text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","last_name":"Lukacisin"},{"first_name":"Matthieu","full_name":"Landon, Matthieu","last_name":"Landon"},{"first_name":"Rishi","last_name":"Jajoo","full_name":"Jajoo, Rishi"}],"department":[{"_id":"ToBo"}],"title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","file_date_updated":"2020-07-14T12:47:02Z","date_updated":"2024-02-21T13:51:53Z","citation":{"mla":"Lukacisin, Martin, et al. MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:45.","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2016). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:45","ama":"Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2016. doi:10.15479/AT:ISTA:45","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016.","short":"M. Lukacisin, M. Landon, R. Jajoo, (2016).","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:45.","ista":"Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:45."},"ddc":["571"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"type":"research_data","keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"status":"public","_id":"5556"},{"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2015-08-13T00:00:00Z","doi":"10.15479/AT:ISTA:28","date_created":"2018-12-12T12:31:29Z","has_accepted_license":"1","year":"2015","day":"13","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"publist_id":"5564","author":[{"last_name":"Fellner","full_name":"Fellner, Andreas","first_name":"Andreas","id":"42BABFB4-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes","citation":{"ama":"Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. 2015. doi:10.15479/AT:ISTA:28","apa":"Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:28","short":"A. Fellner, (2015).","ieee":"A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015.","mla":"Fellner, Andreas. Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria, 2015, doi:10.15479/AT:ISTA:28.","ista":"Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:28.","chicago":"Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015. https://doi.org/10.15479/AT:ISTA:28."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","abstract":[{"lang":"eng","text":"This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees.\r\nThe archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library.\r\nTo execute the program, please have a look at the README.txt, which provides instructions and further information on the archive.\r\nThe archive contains scripts that (if run often enough) reproduces the data presented in the publication."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"popular_science","status":"public","id":"1603"}]},"contributor":[{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kretinsky"}],"ec_funded":1,"datarep_id":"28","file":[{"date_created":"2018-12-12T13:02:31Z","file_name":"IST-2015-28-v1+2_Fellner_DataRep.zip","creator":"system","date_updated":"2020-07-14T12:47:00Z","file_size":49557109,"file_id":"5597","checksum":"b8bcb43c0893023cda66c1b69c16ac62","access_level":"open_access","relation":"main_file","content_type":"application/zip"}],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","keyword":["Markov Decision Process","Decision Tree","Probabilistic Verification","Counterexample Explanation"],"_id":"5549","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:00Z","date_updated":"2024-02-21T13:52:07Z","ddc":["004"]}]