Science	
  Gateways	
  for	
  Life	
  Sciences	
  –	
  
Balancing	
  Usability	
  and	
  Re-­‐Usability	
  
Sandra	
  Gesi...
Life	
  Sciences	
  
“the	
  sciences	
  concerned	
  with	
  the	
  study	
  of	
  living	
  
organisms,	
  including	
  ...
Life	
  Sciences	
  and	
  Computa?on	
  
The	
  Genomics	
  Boom	
  	
  

February	
  16,	
  2001	
  
	
  biotech	
  comp...
Life	
  Sciences	
  and	
  Computa?on	
  	
  	
  
The	
  Genomics	
  Boom	
  	
  

Craig	
  Venter	
  (le`)	
  and	
  Fran...
Areas	
  in	
  the	
  Life	
  Sciences	
  	
  	
  
• 	
  A	
  lot	
  of	
  “omics”	
  sciences,	
  e.g.	
  
• 	
  Genomics...
Molecular	
  Simula?ons	
  and	
  Docking	
  	
  	
  
• 	
  Predic?on	
  and	
  analysis	
  of	
  molecular	
  structures	...
Molecular	
  Simula?ons	
  and	
  Docking	
  	
  	
  
• 	
  Predic?on	
  and	
  analysis	
  of	
  molecular	
  structure	
...
Simula?ons	
  
• 	
  	
  Basic	
  data	
  with	
  heterogeneous	
  provenance,	
  e.g.	
  
	
  Research	
  in	
  Malaria	
...
State-­‐of-­‐the-­‐art	
  
• 	
  	
  Data	
  intensive	
  and	
  compute	
  intensive	
  problems	
  
• 	
  	
  Sophis?cat...
Open	
  Issues	
  
• 	
  Usability	
  of	
  tools	
  o`en	
  limited	
  
• 	
  Complexity	
  of	
  methods	
  
• 	
  Lack	...
Open	
  Issues	
  
• 	
  Usability	
  of	
  tools	
  o`en	
  limited	
  
• 	
  Complexity	
  of	
  methods	
  
• 	
  Lack	...
Open	
  Issues	
  
• 	
  Usability	
  of	
  tools	
  o`en	
  limited	
  

• 	
  Complexity	
  of	
  methods	
  
• 	
  Lack...
Open	
  Issues	
  
• 	
  Usability	
  of	
  tools	
  o`en	
  limited	
  

• 	
  Complexity	
  of	
  methods	
  
• 	
  Lack...
Open	
  Issues	
  
• 	
  Usability	
  of	
  tools	
  o`en	
  limited	
  

• 	
  Complexity	
  of	
  methods	
  
• 	
  Lack...
Open	
  Issues	
  
• 	
  Usability	
  of	
  tools	
  o`en	
  limited	
  

• 	
  Complexity	
  of	
  methods	
  
• 	
  Lack...
Open	
  Issues	
  
• 	
  Usability	
  of	
  tools	
  o`en	
  limited	
  

• 	
  Complexity	
  of	
  methods	
  
• 	
  Lack...
Science	
  Gateways	
  	
  
“A	
  Science	
  Gateway	
  is	
  a	
  community-­‐developed	
  set	
  
of	
  tools,	
  applic...
Web-­‐based	
  Science	
  Gateways	
  	
  
• 	
  Single	
  point	
  of	
  entry	
  
• 	
  Possibility	
  to	
  customize	
...
Goal	
  of	
  Science	
  Gateways	
  	
  
Usability	
  of	
  so`ware	
  
	
  
"AOer	
  all,	
  usability	
  really	
  just...
Re-­‐Usability	
  
•  Sharing	
  of	
  knowledge	
  and	
  data	
  	
  
•  Re-­‐Using	
  of	
  „recipes“	
  and	
  workflow...
Re-­‐Usability	
  
Re-­‐inven?ng	
  is	
  not	
  always	
  necessary...	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  ...
Re-­‐Usability	
  
...	
  but	
  the	
  model	
  should	
  fit	
  to	
  the	
  demands	
  of	
  the	
  
community	
  

Sand...
Diverse	
  Approaches	
  
• 	
  Science	
  gateway	
  frameworks	
  
• 	
  Sta?c	
  layout	
  
• 	
  Layout	
  extendable	...
Galaxy	
  
Python	
  framework	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

24	
  
Galaxy	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

25	
  
Parametriza?on	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

26	
  
Workflows	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

27	
  
Administra?on	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

28	
  
WS-­‐PGRADE	
  
User	
  Interface	
  
WS-­‐PGRADE	
  
Liferay	
  
High-­‐Level	
  
Middleware	
  
Service	
  Layer
	
  
gU...
WS-­‐PGRADE	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

30	
  
Job	
  Configura?on	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

31	
  
Monitoring	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

32	
  
MoSGrid	
  
Molecular	
  Simula?on	
  Grid	
  
• 	
  	
  Science	
  gateway	
  integrated	
  with	
  underlying	
  
	
  co...
Tools	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

34	
  
File	
  Management	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

35	
  
MoSGrid	
  –	
  Applica?on	
  Areas	
  
Molecular	
  Dynamics	
  
• 	
  	
  Study	
  and	
  simula?on	
  of	
  molecular	
...
MD	
  Portlet	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

37	
  
MD	
  Portlet	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

38	
  
MD	
  Portlet	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

39	
  
QC	
  Portlet	
  
	
  
	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

40	
  
QC	
  Portlet	
  
	
  
	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

41	
  
Docking	
  Portlet	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

42	
  
Docking	
  Portlet	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

43	
  
VectorBase	
  	
  	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

44	
  
Tools	
  	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

45	
  
Tools	
  	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

46	
  
Tools	
  	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

47	
  
VECNet	
  	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

48	
  
 Data	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

49	
  
Modeling	
  Plarorm	
  	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

50	
  
Risk	
  Mapper	
  	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

51	
  
Risk	
  Mapper	
  	
  

Sandra	
  Gesing	
  

Science	
  Gateways	
  for	
  Life	
  Sciences	
  

52	
  
Usability	
  vs.	
  Re-­‐Usability	
  
•  User	
  side	
  	
  
•  Methods	
  	
  
•  Workflows	
  	
  
•  Data	
  
è Re-­‐...
Usability	
  vs.	
  Re-­‐Usability	
  
•  User	
  side	
  	
  
•  Layout	
  
•  Visualiza?on	
  	
  
•  Security	
  
è Re...
New	
  Science	
  Gateway	
  -­‐	
  Checklist	
  
• 
• 
• 
• 
• 

Demands	
  of	
  the	
  user	
  community	
  on	
  the	
...
sandra.gesing@nd.edu	
  

Sandra	
  Gesing	
  

Science	
  Gatewazs	
  for	
  Life	
  Sciences	
  

56	
  
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Science Gateways for Life Sciences – Balancing Usability and Re-Usability

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Science Gateways for Life Sciences – Balancing Usability and Re-Usability

  1. 1. Science  Gateways  for  Life  Sciences  –   Balancing  Usability  and  Re-­‐Usability   Sandra  Gesing   Center  for  Research  Compu?ng   sandra.gesing@nd.edu   19  September  2013  
  2. 2. Life  Sciences   “the  sciences  concerned  with  the  study  of  living   organisms,  including  biology,  botany,  zoology,   microbiology,  physiology,  biochemistry,  and  related   subjects”   hMp://www.thefreedic?onary.com     •  Technologies  and  methods  for  crea?ng,  analyzing  and   predic?on  of  data  available   •  Immense  amount  of  data,  e.g.,   •  ZINC  database:  ~20  Mio  molecular  structures     •  Human  genome:  ~  3  Bio  DNA  base  pairs   Sandra  Gesing   Science  Gateways  for  Life  Sciences   2  
  3. 3. Life  Sciences  and  Computa?on   The  Genomics  Boom     February  16,  2001    biotech  company  Celera     Sandra  Gesing   February  15,  2001   The  Human  Genome  Project     Science  Gateways  for  Life  Sciences   3  
  4. 4. Life  Sciences  and  Computa?on       The  Genomics  Boom     Craig  Venter  (le`)  and  Francis  Collins  (right)   Sandra  Gesing   Science  Gateways  for  Life  Sciences   4  
  5. 5. Areas  in  the  Life  Sciences       •   A  lot  of  “omics”  sciences,  e.g.   •   Genomics   •   Proteomics     Black  Swallowtail  -­‐  larvae  and  buMerfly   Sandra  Gesing   Science  Gateways  for  Life  Sciences   5  
  6. 6. Molecular  Simula?ons  and  Docking       •   Predic?on  and  analysis  of  molecular  structures   •   Numerous  applica?ons,  e.g.     •   Materials  science   •   Drug  design       ligands   docking   Sandra  Gesing   target     ?   Science  Gateways  for  Life  Sciences   6  
  7. 7. Molecular  Simula?ons  and  Docking       •   Predic?on  and  analysis  of  molecular  structure   •   Numerous  applica?ons,  e.g.     •   Materials  science   •   Drug  design     ligands   docking   Sandra  Gesing     binding  energy   scoring  func?ons   Science  Gateways  for  Life  Sciences   target   binding   pocket   7  
  8. 8. Simula?ons   •     Basic  data  with  heterogeneous  provenance,  e.g.    Research  in  Malaria   •   Data  on  weather       •   Data  on  demography   •   Data  on  interven?ons   •   ...   •     Mathema?cal  models      needing  a  baseline   •     Predic?on  of      interven?ons   Sandra  Gesing     Science  Gateways  for  Life  Sciences   8  
  9. 9. State-­‐of-­‐the-­‐art   •     Data  intensive  and  compute  intensive  problems   •     Sophis?cated  tools  and  methods  available     •     Distributed  data  management  available   •     DCIs  (Distributed  Compu?ng  Infrastructures)  available         Why  do  researchers  not  use  the  tools  and  distributed   environments  on  a  large  scale?   Sandra  Gesing   Science  Gateways  for  Life  Sciences   9  
  10. 10. Open  Issues   •   Usability  of  tools  o`en  limited   •   Complexity  of  methods   •   Lack  of  graphical  user  interfaces         Sandra  Gesing   Science  Gateways  for  Life  Sciences   10  
  11. 11. Open  Issues   •   Usability  of  tools  o`en  limited   •   Complexity  of  methods   •   Lack  of  graphical  user  interfaces         Sandra  Gesing   Science  Gateways  for  Life  Sciences   11  
  12. 12. Open  Issues   •   Usability  of  tools  o`en  limited   •   Complexity  of  methods   •   Lack  of  graphical  user  interfaces   •   Workflows     steps  in  a  defined  order     a  sequence  of  connected   based  on  their  control     nd  data  dependencies   a   Sandra  Gesing   Science  Gateways  for  Life  Sciences   12  
  13. 13. Open  Issues   •   Usability  of  tools  o`en  limited   •   Complexity  of  methods   •   Lack  of  graphical  user  interfaces   •   Workflows   12181 12241 12301 12361 12421 12481 12541 12601 12661 12721 12781 acatttctac cagtctttta gaccatccta gactaattat taggtgactt aggagctatt ttcttataag tggttaagta tggcattaag atccaatacc taacccattt caacagtgga aattttaacc atagatacac gttgagcttg gcctgttttt tatatattct tctgtggttt tacatgacat tacatccaca cattaagctg tctgtctcta tgaggttgtt tttagagaag agtggtgtct ttaccattta ttttaattgg ggatacaagt ttatattaat aaaacggatt atattgtgca tcactcccca tggatttgcc ggtctatgtt agtcatacag cactgtgatt gacaacttca gatcttaatt tctttatcag gtttttattg atcttaacca actatcacca atctcccatt tgttctggat ctcaccaaat tcaatagcct ttaatttgca ttagagaagt tttttaaatt atacacagtt atgactgttt ttttaaaatg ctatcatact ttcccacccc attcatatta ttggtgttgt tttttagctt ttttcctgct gtctaatatt attgatttgt tgtgactatt tttacaattg taaaattcga ccaaaagggc tgacaatcaa atagaatcaa   steps  in  a  defined  order     a  sequence  of  connected   based  on  their  control     nd  data  dependencies   a   Slide  copied  from:  Stuart  Owen  „Workflows  with  Taverna“   Sandra  Gesing   Science  Gateways  for  Life  Sciences   13  
  14. 14. Open  Issues   •   Usability  of  tools  o`en  limited   •   Complexity  of  methods   •   Lack  of  graphical  user  interfaces   •   Workflows   •   Complexity  of  infrastructures   •   Users  are  generally  not  IT  specialists         Sandra  Gesing   Science  Gateways  for  Life  Sciences   14  
  15. 15. Open  Issues   •   Usability  of  tools  o`en  limited   •   Complexity  of  methods   •   Lack  of  graphical  user  interfaces   •   Workflows   •   Complexity  of  infrastructures   •   Users  are  generally  not  IT  specialists         Sandra  Gesing   Science  Gateways  for  Life  Sciences   15  
  16. 16. Open  Issues   •   Usability  of  tools  o`en  limited   •   Complexity  of  methods   •   Lack  of  graphical  user  interfaces   •   Workflows   •   Complexity  of  infrastructures   •   Users  are  generally  not  IT  specialists     ⇒    User  interfaces  need  to  be  intui8ve  and  self-­‐    explanatory     ⇒  Science  gateways   Sandra  Gesing   Science  Gateways  for  Life  Sciences   16  
  17. 17. Science  Gateways     “A  Science  Gateway  is  a  community-­‐developed  set   of  tools,  applica9ons,  and  data  that  is  integrated   via  a  portal  or  a  suite  of  applica9ons,  usually  in  a   graphical  user  interface,  that  is  further  customized   to  meet  the  needs  of  a  specific  community.”     TeraGrid/XSEDE     Community   Sandra  Gesing   Science  Gateways  for  Life  Sciences   17  
  18. 18. Web-­‐based  Science  Gateways     •   Single  point  of  entry   •   Possibility  to  customize  views  and  tools   •   Store  user  preferences   •   No  installa?on  of  so`ware  on  the  user’s  side     •   No  firewall  issues   Slar9barGast:  “I  must  warn  you,    we're  going  to  pass  through,  well,  a  sort  of   gateway  thing.”   Arthur  Dent:  „What?“   Slar9barGast:  “It  may  disturb  you.  It  scares    the  willies  out  of  me.”   (Douglas  Adams  in  “The  Hitchhiker's  Guide  to  the  Galaxy”)   Sandra  Gesing   Science  Gateways  for  Life  Sciences   18  
  19. 19. Goal  of  Science  Gateways     Usability  of  so`ware     "AOer  all,  usability  really  just  means   that  making  sure  that  something   works  well:  that  a  person  …  can  use   the  thing  -­‐  whether  it's  a  Web  site,  a   fighter  jet,  or  a  revolving  door  -­‐  for  its   intended  purpose  without  geSng   hopelessly  frustrated."     (Steve  Krug  in  “Don't  make  me  think!:  A   Common  Sense  Approach  to  Web  Usability”,   2005)   Sandra  Gesing   Science  Gateways  for  Life  Sciences   19  
  20. 20. Re-­‐Usability   •  Sharing  of  knowledge  and  data     •  Re-­‐Using  of  „recipes“  and  workflows   •  Re-­‐Usability  of  so`ware     “The  key  to  produc9vity  is     reusability.  The  easiest  way  to     produce  code  is  obviously  to     have  it  already!"     (John  R.  Bourne  in  “Object-­‐oriented   Engineering:  Building  Engineering     Systems  Using  Smalltalk-­‐80”,  1992)   Sandra  Gesing   Science  Gateways  for  Life  Sciences   20  
  21. 21. Re-­‐Usability   Re-­‐inven?ng  is  not  always  necessary...   Sandra  Gesing   Science  Gateways  for  Life  Sciences   21  
  22. 22. Re-­‐Usability   ...  but  the  model  should  fit  to  the  demands  of  the   community   Sandra  Gesing   Science  Gateways  for  Life  Sciences   22  
  23. 23. Diverse  Approaches   •   Science  gateway  frameworks   •   Sta?c  layout   •   Layout  extendable   •   Workflow-­‐enabled   •   Portal  frameworks   •   Content  management  systems   •   Libraries  for  implementa?on     Sandra  Gesing   Science  Gateways  for  Life  Sciences   23  
  24. 24. Galaxy   Python  framework   Sandra  Gesing   Science  Gateways  for  Life  Sciences   24  
  25. 25. Galaxy   Sandra  Gesing   Science  Gateways  for  Life  Sciences   25  
  26. 26. Parametriza?on   Sandra  Gesing   Science  Gateways  for  Life  Sciences   26  
  27. 27. Workflows   Sandra  Gesing   Science  Gateways  for  Life  Sciences   27  
  28. 28. Administra?on   Sandra  Gesing   Science  Gateways  for  Life  Sciences   28  
  29. 29. WS-­‐PGRADE   User  Interface   WS-­‐PGRADE   Liferay   High-­‐Level   Middleware   Service  Layer   gUSE   DCI  Resources     Middleware  Layer   Sandra  Gesing   Science  Gateways  for  Life  Sciences   29  
  30. 30. WS-­‐PGRADE   Sandra  Gesing   Science  Gateways  for  Life  Sciences   30  
  31. 31. Job  Configura?on   Sandra  Gesing   Science  Gateways  for  Life  Sciences   31  
  32. 32. Monitoring   Sandra  Gesing   Science  Gateways  for  Life  Sciences   32  
  33. 33. MoSGrid   Molecular  Simula?on  Grid   •     Science  gateway  integrated  with  underlying    compute  and  data  management  infrastructure       •     Distributed  workflow  management   •     Data  repository     Sandra  Gesing   Science  Gateways  for  Life  Sciences   33  
  34. 34. Tools   Sandra  Gesing   Science  Gateways  for  Life  Sciences   34  
  35. 35. File  Management   Sandra  Gesing   Science  Gateways  for  Life  Sciences   35  
  36. 36. MoSGrid  –  Applica?on  Areas   Molecular  Dynamics   •     Study  and  simula?on  of  molecular  mo?on   Quantum  Chemistry   •     Study  and  simula?on  of  molecular  electronic    behavior  rela?ve  to  their  chemical  reac?vity   Docking   •     Main  focus  on  evalua?on  of  ligand-­‐receptor    interac?ons  (e.g.,  for  drug  design)   Sandra  Gesing   Science  Gateways  for  Life  Sciences   36  
  37. 37. MD  Portlet   Sandra  Gesing   Science  Gateways  for  Life  Sciences   37  
  38. 38. MD  Portlet   Sandra  Gesing   Science  Gateways  for  Life  Sciences   38  
  39. 39. MD  Portlet   Sandra  Gesing   Science  Gateways  for  Life  Sciences   39  
  40. 40. QC  Portlet       Sandra  Gesing   Science  Gateways  for  Life  Sciences   40  
  41. 41. QC  Portlet       Sandra  Gesing   Science  Gateways  for  Life  Sciences   41  
  42. 42. Docking  Portlet   Sandra  Gesing   Science  Gateways  for  Life  Sciences   42  
  43. 43. Docking  Portlet   Sandra  Gesing   Science  Gateways  for  Life  Sciences   43  
  44. 44. VectorBase       Sandra  Gesing   Science  Gateways  for  Life  Sciences   44  
  45. 45. Tools     Sandra  Gesing   Science  Gateways  for  Life  Sciences   45  
  46. 46. Tools     Sandra  Gesing   Science  Gateways  for  Life  Sciences   46  
  47. 47. Tools     Sandra  Gesing   Science  Gateways  for  Life  Sciences   47  
  48. 48. VECNet     Sandra  Gesing   Science  Gateways  for  Life  Sciences   48  
  49. 49.  Data   Sandra  Gesing   Science  Gateways  for  Life  Sciences   49  
  50. 50. Modeling  Plarorm     Sandra  Gesing   Science  Gateways  for  Life  Sciences   50  
  51. 51. Risk  Mapper     Sandra  Gesing   Science  Gateways  for  Life  Sciences   51  
  52. 52. Risk  Mapper     Sandra  Gesing   Science  Gateways  for  Life  Sciences   52  
  53. 53. Usability  vs.  Re-­‐Usability   •  User  side     •  Methods     •  Workflows     •  Data   è Re-­‐usability  increases  usability  on  the  user  side   •  Admin/Developer  side   •  Frameworks   •  Libraries   •  Source  code   è Usability  and  re-­‐usability  depend  on  support,          documenta?on  and  scalability       Sandra  Gesing   Science  Gateways  for  Life  Sciences   53  
  54. 54. Usability  vs.  Re-­‐Usability   •  User  side     •  Layout   •  Visualiza?on     •  Security   è Re-­‐used  parts  may  be  not  sufficient,  usability   depends  on  the  features  needed  in  the  community   •  Admin/Developer  side   •  Integra?on  with  compu?ng  and  data  infrastructures   •  Security     è Usability  and  re-­‐usability  depend  on  available   infrastructures     Sandra  Gesing   Science  Gateways  for  Life  Sciences   54  
  55. 55. New  Science  Gateway  -­‐  Checklist   •  •  •  •  •  Demands  of  the  user  community  on  the  user  interface   Demands  on  security   Demands  on  compu?ng  and  data  resources   Workflows   Performance   •  •  •  •  Exis?ng  tools  and  models   Available  underlying  infrastructure   Available  documenta?on  and  support   Effort  on  development  and  maintenance   Sandra  Gesing   Science  Gateways  for  Life  Sciences   55  
  56. 56. sandra.gesing@nd.edu   Sandra  Gesing   Science  Gatewazs  for  Life  Sciences   56  

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