The main objective of the PhD proposal consists of the creation of a platform for IVD Models & Simulations (M&S) tools and their integration into automated workflows, within the HORIZON MSCA Disc4All project. Based on the European Open Science Cloud (EOSC) vision, the expected platform will be a Cloud-based one, furnished with a front-end, to guarantee reproducibility, accessibility and easy use for experts and non-experts. The development of an automated and specialized platform can represent the best hybrid technology with perks on both healthcare data management and computational environments exploitation, given the use of Cloud infrastructures on healthcare software and databases. Though rendering automatic not only the database, but prediction and simulation models in a user-friendly integrated system, may facilitate a difficult diagnosis and forward therapy, especially considering the various forces at play in a multi-omics data analysis of its kind

Codo, Laia

Ferri, Maria Paola

Gelpi, Josep Lluis

English

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Designing a Cloud and HPC Based M&S platformto Investigate the IVD Diseases MechanismsMaria Paola Ferri*1#2, Laia Codo*1, Josep Lluis Gelpi*1#2#1Life Sciences Department, Universitat de Barcelona, Address Including Country Namemferrife108@alumnes.ub.edu, gelpi@ub.edu *2Barcelona Supercomputing Center, Plaza de Usebi Guell 1-3, Barcelona, Spainmaria.ferri@bsc.es, laia.codo@bsc.es, josep.gelpi@bsc.es Keywords— BioBB, Intervertebral Disc Degeneration, Workflow Framework, Portable PlatformI. EXTENDED ABSTRACTThe  main  objective  of  the  PhD  proposal  consists  of  thecreation of a platform for IVD Models & Simulations (M&S)tools  and  their  integration  into  automated  workflows,  withinthe HORIZON MSCA Disc4All project.Based on the European Open Science Cloud (EOSC) vision,the  expected  platform  will be  a  Cloud-based  one,  furnishedwith a front-end, to guarantee reproducibility, accessibility andeasy use for experts and non-experts.The development of an automated and specialized platformcan represent  the best  hybrid technology with perks  on bothhealthcare data management and computational environmentsexploitation,  given  the  use  of  Cloud  infrastructures  onhealthcare software and databases. Though rendering automaticnot only the database, but prediction and simulation models ina  user-friendly  integrated  system,  may  facilitate  a  difficultdiagnosis  and  forward  therapy,  especially  considering  thevarious forces at play in a multi-omics data analysis of its kind.A. IntroductionLBP  (Low  Back  Pain)  is  the  largest  cause  of  morbidityworldwide,  yet  there  remains  undetected  the  liable  specificcause, leading to poor treatment options and prognosis. As forother  highly  multi-factorial  musculoskeletal  (MS)  disorders,such  as  lumbar  intervertebral  disc  (IVD)  and  Lumbar  DiscDegeneration (LDD), the interplay of a wide range of factors ispoorly understood. Some genetic factors have been identifiedas  possible  biomarkers  of  specific  LDD phenotype,  such  asInterleukin (IL)-, ECM protein- and protease-related genes, aswell  as  human  genetic  variants  (GDF5,  SKT,  PARK2  andCHST3)[1].  Beyond molecular  data,  also nutritional,  clinical,social  conditions  are  at  stake  for  such  diagnosis:  molecularprofiling,  medical  imaging,  lifestyle  data,  sex  are  crucialfactors  to determine  the predisposition of  a  single patient  tothese multi-factorial disorders[2].Unfortunately, the integration of such data into a holistic andrational map of degenerative processes and risk factors has notbeen  achieved,  requiring  the  creation  of  professional  crosscompetencies training programs.The  HORIZON  MSCA  Disc4All  project  is  proposing  toprovide for an interdisciplinary solution to make up for the lackof  diagnosis  tools  and  instruments,  considering  all  thebiological,  medical  and  computational  contributions.  Thecuration and integration of all the heterogeneous data sets, aswell  as  experimental  and  theoretical/computational  templateand  algorithms,  are  going  to  be  embedded  to  exploit  themultidisciplinary and multiscale models and simulations tools,based on image analysis, biophysics and biology[ 14 ].B. MethodsThe ultimate purpose  of this Disc4All  final  infrastructure,deployed on the biological,  bioinformatics  algorithms, imageanalysis  and  ML/AI  models  and  tools,  is  to  integrate  andinterpolate  primary  patient  data  and  achieve  a  coherentattribution of a MS phenotype.To get a homogeneous configuration between all the tools,the  first  and  main  aim  of  the  project  is  to  contain  all  theworkflow  tools  into  a  similar  framework.  This  would  bereached  through  the  use  of  the  BioExcel  Building  Blocks(BioBBs)[3],  a  collection  of  Python  wrappers  on  top  ofbiomolecular/  bioinformatics  simulation  tools.  With  theirmutual  unique  syntax,  they  offer  a  layer  of  interoperabilitybetween the wrapped tools, to make their interconnection easierin  the  building  process  of  a  biomolecular/bioinformaticsworkflow. The  BioBBs also  allow singular  deployment  of  each  toolwithin  a  Docker  bio-container,  but  will  also  be  assessed  aprivate Cloud resource and its own Disc4All instantiation. Sharing this technology, the tools produced for the Disc4allproject would be effortlessly combined in the most convenientand  comprehensive  way,  through  the  CWL  (CommonWorkflow  Language)  or  any  other  convenient  workflowmanager language.Fig. 1  BioBB’s Automated deployment strategy[3]In the end, thanks to the BioBBs adaptation layer, there aremany  possibilities  for  exposing  the  BioBB based  workflow,such as Galaxy, Jupyter Notebooks, etc. One of the strategiesfor  the  front-end  display  is  the  web-server  VRE  (VirtualResearch Environment)[³]. It will be exploited to construct thefront-end of the infrastructure, so to provide for the non-expertusers an easy-to-use platform to perform their analysis with thecontainerized pipeline.43C. Discussion and ResultsThe  platform  will  provide  the  necessary  environment  todevelop workflows using the tools developed in the Disc4Allproject. The current objective for the development of the platform isthe  adaptation  of  the  tools  and  software,  given  theircomputation and data requirements, into BioBBs.  Since moreof the half of the tools are in development,  the best course ofaction is to start for each of them a single BioBB instantiation,so  as  to  first  define  the  basic  pre-processing  steps  andenvironment. This introductory BioBBs are in production, onefor  Genomics  data  retrieval  and  the  other  one  for  a  pre-Learning Active Cycle extracting features from imaging data.  Different  modular  Cloud containers  are deployed for  eachBioBB,  to  have  independent  environments  that  could  bepossibly  concatenated,  following  official  FAIR  workflowstandards. On  one  of  them,  the  first  draft  for  the  final  front-endplatform is instantiated and exposed, in compliance with theopenVRE environment. It is furnished with a simple case-useof  the  project  (which  is  the  aforementioned  pre-processingBioBB data retrieval), that is up and working. This preliminaryinterface  then  is  going to  be completed with the rest  of  thetools, that could be called individually, and with the integralpipeline. D. Future EnhancementIn the foreseeable future, the work on the adaptation to theBioBB framework will continue with the advancement of thetools,  as  well  as  the  exploration  of  federated  data  accessstrategies with the furnished data model,  for smooth flow ofinformation through the platform, as  well  as  exploring otherdata models adapters.For the long term results, should be taken due account thedifferent  types  of  instantiations  on  Cloud-based  and  HPCenvironments, to build the computational infrastructure throughDocker  &  EOSC  cloud-based  services,  such  as  BSC’sMareNostrum  or  StarLife  (for  users  with  granted  HPCcredentials),  and  to  be  able  to  probe  the  perks  of  hybridworkflows.The front-end is  a  key point  for  the users  (end-users  anddevelopers), to render available the workflow in the appropriatecomputational  environments,  so  its  finalization  would  becarried out in conformity with the progression of the study. E. ACKNOWLEDGMENTSThis  project  is  part  of  the  Disc4All  Training  network  toadvance  integrated  computational  simulations in  translationalmedicine,  applies  to  intervertebral  disc  degeneration  andfunded by Horizon 2020 (H2020-MSCA-ITN-ETN-2020 GA:955735).I'd  want  to  convey  my  appreciation  and  gratitude  to  mysupervisors and co-supervisor for providing me with the chanceto work and learn from them in their  welcoming group.  I’dwant  also  to  thank  my  fellow  colleagues  and  PIs  from  theDisc4All group, for their contribution and collaboration. References  [1] Gantenbein  B,  May  RD,  Bermudez-Lekerika  P,  OswaldKAC, Benneker LM, Albers CE (2021) EGR2, IGF1 andIL6 Expression Are Elevated in the Intervertebral Disc ofPatients  Suffering  from  Diffuse  Idiopathic  SkeletalHyperostosis  (DISH)  Compared  to  Degenerative  orTrauma  Discs.  Applied  Sciences  11(9):https://doi.org/10.3390/app11094072[2] Eskola, P. J. et al. Gender difference in genetic associationbetween IL1A variant and early lumbar disc degeneration:A three-year follow-up. Int. J. Mol. Epidemiol. Genet. 3,195–204 (2012) [3] BioExcel  Building  Blocks,  a  software  library  forinteroperable  biomolecular  simulation  workflows.  PauAndrio, Adam Hospital, Javier Conejero, Luis Jordá, MarcDel Pino, Laia Codo, Stian Soiland-Reyes, Carole Goble,Daniele Lezzi, Rosa M. Badia, Modesto Orozco & JosepLl. Gelpi. Nature Scientific Data, 09/2019,Volume 6, Issue1, p.169, (2019).[4] Towards FAIR principles for research software, LamprechtAnna-Lena, Garcia Leyla, Kuzak Mateusz,Martinez  Carlos,  Arcila  Ricardo,  Martin  Del  Pico  Eva,Dominguez Del Angel Victoria, van de Sandt Stephanie,Ison  Jon,  Martinez  Paula  Andrea,  McQuilton  Peter,Valencia Alfonso. Harrow Jennifer. Psomopoulos Fotis,Gelpi Josep Ll., Chue Hong Neil, Goble Caroleu, Capella-Gutierrez, Salvador. 10.3233/DS-190026. DataScience, vol. Pre-press, no. Pre-press, pp. 1-23, 2019[5] Felipe da Veiga Leprevost, Björn A Grüning, Saulo AlvesAflitos, Hannes L Röst, Julian Uszkoreit, Harald Barsnes,Marc Vaudel, Pablo Moreno, Laurent Gatto, Jonas Weber,Mingze  Bai,  Rafael  C  Jimenez,  Timo  Sachsenberg,Julianus Pfeuffer,  Roberto Vera Alvarez,  Johannes Griss,Alexey  I  Nesvizhskii,  Yasset  Perez-Riverol,BioContainers:  an  open-source  and  community-drivenframework  for  software  standardization, Bioinformatics,Volume  33,  Issue  16,  15  August  2017,  Pages  2580–2582, https://doi.org/10.1093/bioinformatics/btx192 Author biography Maria Paola Ferri  was born in  Rome,Italy, in 1995.  She graduated in 2018 inBiotechnologies,  from  the University ofRome La  Sapienza,  and  in  2021  sheobtained the Internation Master degree inBioinformatics  from  the AlmaMater University  of Bolumn. Her  masterthesis  was  focused  on  the  creation  ofCloud  architectures designed  to support  and  instantiateBioinformatics applications, curing the portability and the user-friendly access to them. Right now, she is holding a position inthe  Life  Science's  Department  at  the  BSC  (BarcelonaSupercomputing  Center). Her  role  in  the  Disc4All  projectwould  be  to  extend  the  implementation  of  the IDDidentification  and  prediction software  in  development  into  aCloud and HPC environment, so to create in the end a portableand  ready-to-use  front-end  workflow in  the  LBP  (low  backpain) investigation, for user and non-experts.44

Designing a cloud and HPC based M&S platform to Investigate the IVD diseases mechanisms

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Designing a cloud and HPC based M&S platform to Investigate the IVD diseases mechanisms

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