Presentations & Posters

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Presentations

  1. Metabolomics data analysis in the context of metabolomics data,  Training on data analysis of metabolomics data, South Africa, March 2018.
  2. The Elixir metabolomics community and implementation study on metabolite identification, 12th CeBiTec symposium 2018, Big data in Medicine and Biotechnology, Bielefeld, March 2018.
  3. Deploy PhenoMeNal with KubeNow, EOSC Hub All Hands Meeting, Spain, March 2018
  4. Hitchhikers Guide to CompMS, LRC Summer School “High Throughput Screening of Enzymes”, Halle, March 2018.
  5. Cloud 101 and PhenoMeNal Overview, denbi Winter School, Germany, March 2018
  6. Metabolomics, Cloud 101 and PhenoMeNal Overview Workshop, U. Minho Bioinformatics Master’s Bioinformatics Week, Portugal, March 2018.
  7. nmrML, an open access NMR raw data standard supported by Workflows, German NMR Conference, Mainz, March 2018.
  8. Galaxy tools and workflows for metabolomics: A community effort to make data processing and analysis accessible, reproducible, and transparent, Galaxy community kickoff meeting and Galaxy User Conference, Freiburg, March 2018.
  9. Using Galaxy workflows for metabolomics, EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists, February 2018, EMBL-EBI, Cambridge, UK.
  10. Statistical workflows with Galaxy, PhenoMeNal Gateway workshop, December 2017, Birmingham, UK
  11. nmrML: An open vendor-neutral data exchange format for NMR metabolomics, MetaboMeeting 2017, December 2017, Birmingha, UK.
  12. Overcoming acquired drug resistance driven by metabolic reprogramming in colorectal cancer: CDK4/6 as a model target, MetaboMeeting 2017, December 2017, Birmingham, UK.
  13. Metabolomics in the Cloud: Scaling Computational Tools to Big Data,  MetaboMeeting 2017, December 2017, Birmingham, UK.
  14. Advancing metabolomics towards regulatory applications in human and environmental toxicology, MetaboMeeting 2017, December 2017, Birmingham, UK.
  15. Overcoming acquired drug resistance driven by metabolic reprogramming in colorectal cancer: CDK4/6 as a model target, MetaboMeeting 2017, December 2017, Birmingham, UK
  16. PhenoMeNal: Virtual Research Environments for Metabolomics as a use case in Tryggve2, NeIC Tryggve2 Kickoff, November 2017, Stockholm, Sweden.
  17. Data-intensive applications on cloud computing resources: Applications in life sciences,  de.NBI Symposium 2017 “The Future Development of Bioinformatics in Germany and Europe”, October 2017, Bielefeld, Germany.
  18. Scalable and reproducible workflows with Pachyderm,COST-CHARME ‘Big Data Training School for Life Sciences, 18-22 September 2017 in Uppsala, Sweden.
  19. Large-scale clinical metabolomics using mass spectrometry, COST-CHARME ‘Big Data Training School for Life Sciences, 18-22 September 2017 in Uppsala, Sweden
  20. biodb R package: a unified framework to access biological and chemical databases, International conference on bioinformatics and computational biology (BBCC2017), 18-20 Dec. 2017, Naples.
  21. Scalable and reproducible workflows with Pachyderm, DevFest Siberia 2017, 23-24 Sept 2017, Novosibirsk, Russia.
  22. KubeNow: A cloud agnostic platform for microservice-oriented applications, Imperial College Computing Student Workshop (ICCWS2017), October 2017, London UK.
  23. KubeNow: A cloud agnostic platform for microservice-oriented applications, OpenRiskNet workshop on microservice development, September 2017, Uppsala, Sweden
  24. Who to follow? Recommendation systems used to improve metabolic profiling of Hepatic Encephalopathy, EUSTM 2017, European Society of Translational Medecine conference, October 2017, Berlin.
  25. Connecting virtual research environments and large scale compute resources, 23rd November 2017, Utrect, Netherlands
  26. COST-CHARME ‘Big Data Training School for Life Sciences’, 18-22 September 2017 in Uppsala, Sweden.
  27. Automating Galaxy Workflow Testing, BITS 2017: 14th Annual Meeting of the Bioinformatics Italian Society, July 2017, Cagliari, Italy. Click here to view
  28. PhenoMeNal:Large scale computing for medical metabolomics, ResOps: Delivering Science Across Clouds, July 2017, EMBL-EBI, UK.
  29. Metabolomics in the cloud, DeNBI summer school on cloud computing, June 2017, Giessen, Germany.
  30. Hitchhikers Guide to Computational Mass Spectrometry, 2nd NatMedDay, June 2017, Sansepolcro, Italy.
  31. Statistical workflows and tutoring, Workflow4Experimenters 2017, June 2017, Paris, France.
  32. Bayesian deconvolution of NMR spectra with BATMAN, Workflow4Experimenters 2017, June 2017, Paris, France.
  33. Optimised analytical and computational methods for direct-infusion mass spectrometry-based metabolomics, Workflow4Experimenters 2017, June 2017, Paris, France.
  34. Combining text mining and metabolic network algorithms to complement and interpret metabolic profiles,  Metabolomics 2017, June 2017, Brisbane, Australia.
  35. Metabolomics in the cloud using workflows: the PhenoMeNal approach,  Metabolomics 2017, June 2017, Brisbane, Australia.
  36. Substance class annotation for long candidate lists in metabolite identification using structural ontologies, Metabolomic 2017, June 2017, Brisbane Australia.
  37. Data management in Metabolomics, Inserm – Management and reuse of health data: methododical issues, May 2017, Bordeaux, France.
  38. Substance class annotation for long candidate lists in metabolite identification using structural ontologies, Central German Conference on Bioinformatics, May 2017, Leipzig, Germany.
  39. Power and Sample Size Calculations in Metabolomics, Workflow4Experimenters 2017, June 2017, Paris, France.
  40. The case for cloud computing in Life Sciences, CloudBeer 2017, March 2017, Uppsala, Sweden.
  41. Using Tracer Based Approaches to Study Metabolism in Mammalian Cells, 25th anniversary of the Swedish NMR Facility, October 2016, Gothenburg, Sweden.
  42. Big Data in Life Sciences Research, Informatics & Media department research seminars, November 2016, Uppsala Sweden.
  43. Metabolite Annotation & Sharing Halle, de.NBI SAB Meeting, November 2016, Berlin, Germany.
  44. Analyzing Big Data in Medicine with Virtual Research Environments and Microservices, Big Data in Medicine, November 2016, Uppsala Sweden.Analyzing Big Data in Medicine with Virtual Research Environments and Microservices from Uppsala University
  45. PhenoMeNal – Large scale computing for medical metabolomics, RCUK Cloud Working Group Workshop, November 2016. The workshop was intended to bring together researchers and technical specialists to share expertise in the application of cloud computing technology for the research community. Click here to view.                                                                                        
  46. Data sharing, standards and workflows in metabolomics; towards reproducibility in Metabolomics, A combined CHARME, EMBnet and NETTAB 2016 Workshop, Rome, Italy.
  47. PhenoMeNal: Large Scale Computing for Medical Metabolomics, Genome Campus Software Craftsmanship Community, 2016, EMBL-EBI, UK. The presentation describes the work done in the context of containerising metabolomics software tools and running them on top of a container orchestrator environment (Google Kubernetes), a cluster for containers that can be deployed on scalable infrastructure. Click here to view.
  48. Interoperability and scalability with microservices in science, OpenTox Euro, 2016, Rheinfelden, Germany. Click here to view.
  49. Processing Mass-Spectrometry data with Galaxy in a cloud environment, 3rd Swiss Galaxy Workshop, 2016, Freiburg, Germany.
  50. Identification of the metabolic reprogramming underlying metastasis: use and development of PheNoMenal e-infrastructures for analyzing metabolic phenotype data, 1st Conference of the EuropeanAssociation of Systems Medicine, October 2016, Berlin, Germany. Click here to view
  51. PhenoMeNal: Large Scale Computing for Medical Metabolomics, CORBEL General meeting, October 2016, Graz, Austria. Click here to view
  52. High(er)-throughput metabolite annotation, Max Rubner Conference 2016: Food Metabolomics, October 2016, Karlsruhe, Germany.
  53. Towards standardized evidence descriptors for metabolite annotations, Ontologies and Data in Life Sciences (ODLS), September 2016, Halle, Germany. Click here to view
  54. Identification of the metabolic reprogramming underlying metastatic potential by model-driven multi-omic data analysis unveils new putative drug targets, International Conference on Systems Biology (ICSB), September 2016, Barcelona, Spain.
  55. PhenoMeNal: Large Scale Computing for Medical Metabolomics, Industry Programme Quarterly Meeting, September 2016, EMBL-EBI, UK.The presentation was part of the quarterly meeting for EMBL-EBI Industry Programme. Click here to view
  56. Workshop on Virtual research environments for the Open Science Cloud, Digital Infrastructures for Research, September 2016, Krákow, Poland.
  57. Genome scale network modelling, from observations to predictions, Metabolism & Cancer Symposium, 2nd edition, French Canceropole, September 2016, Montpellier, France. Click here to view.
  58. Deciphering cancer metabolism using NMR, 8th GERMN / 5th Iberian NMR Meeting, June 2016, Valencia, Spain.
  59. PhenoMeNal H2020 project: A gateway to personalised medicine, Metabolic phenotyping in clinical practice, May 2016, Barcelona. The workshop was hosted by the PhenoMeNal consortium to define the state-of-the-art in Metabolic Phenotyping in the clinic. The event was attended by a mixed audience from medical/clinical, industry or commercial, government, working or collaborating  using metabolomics data and tools and technologies related to clinic. Click here to view                                                                                                                               
  60. PhenoMeNal: A comprehensive and standardised e-infrastructure for analysing medical phenotype data, PhenoMeNal Industry Workshop, June 2016, Dublin. The workshop was hosted during the Metabolomics Conference in Dublin with an aim to create a lasting interaction with the industy, in order to raise awareness of the PhenoMeNal initiative and to ensure optimal interoperability of PhenoMeNal infrastructure and instrument vendor’s data formats and tools. Click here to view
  61. MetExplore and Genome-Scale metabolic networks, MetaboMeeting, December 2015, Cambridge, UK
  62. The Workflow4Metabolomics computational infrastructure: meeting the workflow challenge  MetaboMeeting, December 2015, Cambridge.
  63. Does LC/MS metabolomics metabolite annotation make sense for imaging MS,  Mass spectrometry imaging – challenges and opportunities for next-generation capabilities, RSC workshop, November 2015, Buckinghamshire.
  64. Sharing data from clinical and medical research, Workshop Data Sharing for Advancing Health, BioMedBridges Symposium, November 2015, Cambridge, UK.
  65. PhenoMeNal – e-infrastructure for clinical metabolomics, RDA Plenary Meeting, September 2015, Paris.

Posters

  1. Large Scale Computing for Medical Metabolic Phenotyping Data, EMBL-EBI day, May 2017, Cambridge, UK
  2. MetExploreViz: Visualisation of metabolic online, French Regional Bioinformatics Conference, December 2016, Toulouse, France.
  3. EasyMapReduce: Leverage Docker and Spark to Scale Any Data Processing Tool in MapReduce Fashion, Swedish e-Science Academy, October 2016, Lund, Sweden.
  4. Dynamic Scientific Workflows in Drug Discovery, Swedish e-Science Academy, October 2016, Lund, Sweden.
  5. Scalable genomics From Raw Data to Aligned Reads on Apache Yarn, Big Data in Biology and Health, Heidelberg, Germany.
  6. Workflows for fluxomics in the framework of PhenoMeNal project,  International Study Group for Systems Biology (ISGSB) meeting, October 2016, Jena.
  7. Workflows for fluxomics in the framework of PhenoMeNal project, ICSB, September 2016, Barcelona.
  8. Achieving accurate reproducible results and computational challenges in large scale untargeted metabolomic studies, CAC 2016, Barcelona.
  9. Iso2Flux: A new software for 13C fluxomics developed in the framework of PheNomeNal, Metabolomics Conference 2016, Dublin.
  10. Scalable analysis setup enables high-throughput metabolites, Metabolomics Conference 2016, Dublin.
  11. Metabomatching: A tool for untargeted identification of genetically influenced metabolites, Metabolomics Conference 2016, Dublin.
  12. PhenoMeNal – Large Scale Computing for Medical Metabolic Phenotyping Data, Metabomeeting 2015, Cambridge.
  13. A Dynamic Model of Metabolism that Integrates 13C Isotopomer Data, Conference on Constraint-Based Reconstruction and Analysis (COBRA 2015). September, 2015. Heidelberg, Germany

 Zenodo Community – PhenoMeNal-H2020 project

View deliverables and presentations