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First	
  Workshop	
  on	
  Maintainable	
  
So3ware	
  Prac7ces	
  in	
  e-­‐Science	
  
                       Neil	
  Chue	
  Hong	
  
                      So3ware	
  Sustainability	
  Ins7tute	
  

                       Jennifer	
  Schopf	
  
                            IEEE	
  Computer	
  Society	
  


   hDp://www.so3ware.ac.uk/maintainable-­‐so3ware-­‐prac7ce-­‐workshop	
  
Published	
  online	
  13	
  October	
  2010	
  |	
  Nature	
  467,	
  775-­‐777	
  (2010)	
  	
  
doi:10.1038/467775a	
  
Stopping	
  errors	
  before	
  they	
  maDer	
  
•  Errors	
  unchecked	
  in	
  code	
  cause	
  retrac7ons	
  

•  Chang	
  –	
  Protein	
  Structure	
  
     –  Error	
  in	
  data	
  analysis	
  code	
  flipped	
  two	
  
        columns	
  of	
  	
  inver7ng	
  electron	
  density	
  map	
  
     –  Science	
  22	
  December	
  2006:	
  Vol.	
  314	
  no.	
  
        5807	
  pp.	
  1856-­‐1857	
  DOI:	
  10.1126/science.
        314.5807.1856	
  

•  Bertoia	
  –	
  Hypertension	
  
     –  Error	
  in	
  code	
  led	
  to	
  doubling	
  of	
  sample	
  size	
  
        and	
  significantly	
  different	
  es7mates	
  
     –  Hypertension.	
  2012;60:e29,	
  published	
  
        online	
  before	
  print	
  August	
  6	
  2012,	
  doi:
        10.1161/HYP.0b013e318269bc7a	
  
Ensuring	
  so3ware	
  is	
  maintained	
  
    •  OU	
  Knowledge	
  Network	
  
           –  All	
  funding	
  stopped	
  a3er	
  8	
  
              years,	
  with	
  11,000	
  ac7ve	
  
              users	
  –	
  s7ll	
  available	
  
    •  Atmospheric	
  Model	
  
           –  Upgrades	
  to	
  hardware	
  
              meant	
  so3ware	
  did	
  not	
  
              run	
  –	
  took	
  effort	
  to	
  
              address	
  	
  
So3ware	
  Preserva7on	
  Benefits	
  Framework:	
  	
  
hDp://www.so3ware.ac.uk/aDach/So3warePreserva7onBenefitsFramework.pdf	
  
A	
  typical	
  e-­‐Science	
  project	
  
                    organisa7on?	
  

       Steering	
  Group	
  


                                                                InvesJgators	
  
        Project	
  Managers	
     10	
  partners	
  




                                                           Researchers	
  

Developers	
  
                                                       Students	
  
Topics	
  of	
  Interest	
  
•  So3ware	
  engineering	
  and	
  so3ware	
  product	
  management	
  best	
  
   prac7ce	
  as	
  applied	
  to	
  e-­‐Science	
  and	
  computa7onal	
  science	
  
•  Community	
  development,	
  collabora7ve	
  development,	
  and	
  
   widening	
  adop7on	
  
•  Licensing,	
  funding,	
  and	
  business	
  models	
  for	
  eScience	
  and	
  research	
  
   so3ware	
  
•  Managing	
  governance	
  and	
  organisa7onal	
  change	
  during	
  the	
  
   so3ware	
  lifecycle	
  
•  Measuring	
  and	
  analysing	
  the	
  impact	
  of	
  so3ware	
  and	
  so3ware	
  
   processes	
  
•  So3ware	
  aDribu7on,	
  cita7on,	
  and	
  credit	
  
•  Interac7on	
  between	
  researchers,	
  developers	
  and	
  stakeholders	
  
•  Transferable	
  so3ware	
  prac7ces	
  from	
  industry	
  
Agenda	
  –	
  morning	
  
             Communi7es	
  and	
  Prac7ces	
  
•  09:00 	
  Introduc7on	
  to	
  the	
  Workshop	
  
•  09:30 	
  Sustainable	
  So3ware	
  for	
  Computa7onal	
  Chemistry	
  	
  
   	
   	
   	
  and	
  Materials	
  Modeling	
  
•  10:00 	
  Break	
  
•  10:30 	
  Adop7on	
  of	
  So3ware	
  by	
  a	
  User	
  Community:	
  The	
  	
  
   	
   	
   	
  Montage	
  Image	
  Mosaic	
  Engine	
  Example	
  
•  11:00 	
  On	
  Realizing	
  the	
  Concept	
  Study	
  ScienceSo3	
  of	
  the	
  	
  
   	
   	
   	
  European	
  Middleware	
  Ini7a7ve	
  -­‐	
  OpenSo3ware	
  for	
  	
  
   	
   	
   	
  Open	
  Science	
  
•  11:30 	
  The	
  Rela7onship	
  Between	
  Development	
  Problems	
  	
  
   	
   	
   	
  and	
  Use	
  of	
  So3ware	
  Engineering	
  Prac7ces	
  in	
  	
  
   	
   	
   	
  Computa7onal	
  Science	
  
•  12:00 	
  Lunch	
  
Agenda	
  –	
  a3ernoon	
  
                     Models	
  and	
  Methods	
  
•  13:30       	
  libHPC:	
  So3ware	
  sustainability	
  and	
  reuse	
  	
  
   	
   	
     	
  through	
  metadata	
  preserva7on	
  
•  14:00       	
  Overview	
  of	
  the	
  TriBITS	
  Lifecycle	
  Model	
  
•  14:30       	
  IPOL:	
  Reviewed	
  Publica7on	
  and	
  Public	
  	
  
   	
   	
     	
  Tes7ng	
  of	
  Research	
  So3ware	
  	
  
   	
   	
     	
  Debate	
  introduc7on	
  
•  15:00       	
  Break	
  
•  15:30       	
  Culture	
  Change	
  debate:	
  "What	
  can	
  we	
  do	
  	
  
   	
   	
     	
  to	
  change	
  the	
  status	
  quo?	
  Should	
  we	
  do	
  this?”	
  
•  17:00       	
  Close	
  
Area	
  of	
  Interest	
  from	
  Audience	
  
•  Prac7ces	
  and	
  models	
                    •  Mixed	
  industry/academic	
  projects	
  
•  Portability	
  across	
  heterogeneous	
       •  Integra7on	
  of	
  so3ware	
  
   plalorms	
                                        components	
  
•  Ways	
  of	
  reducing	
  complexity	
         •  Sustaining	
  so3ware	
  on	
  liDle	
  
•  Recording	
  informa7on	
  on	
                   money	
  
   so3ware	
  structure	
                         •  So3ware	
  engineering	
  applied	
  to	
  
•  Making	
  so3ware	
  verifiable	
                  computa7onal	
  science	
  
•  Building	
  communi7es	
  around	
             •  Is	
  there	
  a	
  life	
  beyond	
  public	
  
   so3ware	
                                         funding	
  (e.g.	
  for	
  dCache)?	
  
•  Cultural	
  issues	
  in	
  organisa7ons	
     •  So3ware	
  +	
  data	
  preserva7on	
  for	
  
•  Collabora7on	
  between	
                         10	
  years	
  usage	
  (e.g.	
  Tevatron)	
  	
  
   ins7tu7ons	
  and	
  countries	
               •  Taking	
  responsibility	
  for	
  orphaned	
  
•  Meta-­‐issues	
  of	
  so3ware	
  across	
        so3ware	
  (e.g.	
  for	
  OSG)	
  
   science	
  and	
  social	
  science	
          •  Understanding	
  what	
  so3ware’s	
  
                                                     been	
  funded	
  and	
  what’s	
  
                                                     happened	
  to	
  it?	
  
Culture	
  Change	
  Discussion	
  
•  Goals	
  
    –  Understand	
  what	
  are	
  the	
  key	
  barriers	
  to	
  culture	
  
       change	
  with	
  respect	
  to	
  so3ware	
  in	
  research	
  
    –  Understand	
  who	
  and	
  what	
  needs	
  to	
  change,	
  to	
  
       change	
  the	
  status	
  quo	
  
    –  Record	
  the	
  studies,	
  examples,	
  prac7ces	
  and	
  
       models	
  that	
  the	
  workshop	
  par7cipants	
  agree	
  
       should	
  be	
  highlighted	
  
Ques7ons	
  
1  What	
  are	
  the	
  basic	
  so3ware	
  skills	
  and	
  
   understanding	
  every	
  scien7st	
  needs?	
  
   –  Beverly	
  Sanders	
  et	
  al.	
  
2  Life	
  beyond	
  public	
  grant	
  funding	
  –	
  what	
  happens	
  
   next?	
  
   –  Bruce	
  Berriman,	
  Michael	
  McLennan,	
  Jennifer	
  Schopf,	
  
      Nigel	
  Ward,	
  Jim	
  Willenbring	
  
3  So3ware	
  reward,	
  cita7on,	
  aDribu7on.	
  Tracking	
  
   usage	
  and	
  impact	
  
   –  Neil	
  Chue	
  Hong,	
  Alberto	
  Di	
  Meglio,	
  Josh	
  Greenberg,	
  
      Juan	
  Lalinde,	
  Kevin	
  Jorissen	
  
Process	
  
•  Brainstorm	
  issues	
  and	
  ideas	
  (45	
  mins,	
  around	
  break)	
  
     –  Put	
  down	
  ideas	
  without	
  judgement	
  (it	
  doesn’t	
  maDer	
  if	
  
        someone	
  else	
  doesn’t	
  think	
  it’ll	
  work)	
  
     –  If	
  you’ve	
  heard	
  of	
  something,	
  write	
  it	
  down	
  
•  Understand	
  and	
  group	
  (15	
  mins)	
  
     –  Do	
  you	
  have	
  the	
  same	
  understanding	
  of	
  all	
  the	
  ideas	
  
     –  Are	
  some	
  of	
  the	
  ideas	
  linked	
  
•  Priori7se	
  and	
  record	
  (30	
  mins)	
  
     –  What	
  are	
  the	
  biggest	
  issues?	
  
     –  What	
  are	
  the	
  ideas	
  that	
  you’ve	
  seen	
  that	
  (don’t)	
  work	
  best?	
  
     –  Are	
  there	
  trends/correla7ons	
  that	
  should	
  be	
  explored?	
  
•  Share	
  your	
  findings	
  (15	
  mins)	
  
•  Please	
  record	
  digitally	
  so	
  that	
  it	
  can	
  be	
  easily	
  shared	
  

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Maintainable Software Practices for e-Science - Introduction to Workshop

  • 1. First  Workshop  on  Maintainable   So3ware  Prac7ces  in  e-­‐Science   Neil  Chue  Hong   So3ware  Sustainability  Ins7tute   Jennifer  Schopf   IEEE  Computer  Society   hDp://www.so3ware.ac.uk/maintainable-­‐so3ware-­‐prac7ce-­‐workshop  
  • 2. Published  online  13  October  2010  |  Nature  467,  775-­‐777  (2010)     doi:10.1038/467775a  
  • 3. Stopping  errors  before  they  maDer   •  Errors  unchecked  in  code  cause  retrac7ons   •  Chang  –  Protein  Structure   –  Error  in  data  analysis  code  flipped  two   columns  of    inver7ng  electron  density  map   –  Science  22  December  2006:  Vol.  314  no.   5807  pp.  1856-­‐1857  DOI:  10.1126/science. 314.5807.1856   •  Bertoia  –  Hypertension   –  Error  in  code  led  to  doubling  of  sample  size   and  significantly  different  es7mates   –  Hypertension.  2012;60:e29,  published   online  before  print  August  6  2012,  doi: 10.1161/HYP.0b013e318269bc7a  
  • 4. Ensuring  so3ware  is  maintained   •  OU  Knowledge  Network   –  All  funding  stopped  a3er  8   years,  with  11,000  ac7ve   users  –  s7ll  available   •  Atmospheric  Model   –  Upgrades  to  hardware   meant  so3ware  did  not   run  –  took  effort  to   address     So3ware  Preserva7on  Benefits  Framework:     hDp://www.so3ware.ac.uk/aDach/So3warePreserva7onBenefitsFramework.pdf  
  • 5. A  typical  e-­‐Science  project   organisa7on?   Steering  Group   InvesJgators   Project  Managers   10  partners   Researchers   Developers   Students  
  • 6. Topics  of  Interest   •  So3ware  engineering  and  so3ware  product  management  best   prac7ce  as  applied  to  e-­‐Science  and  computa7onal  science   •  Community  development,  collabora7ve  development,  and   widening  adop7on   •  Licensing,  funding,  and  business  models  for  eScience  and  research   so3ware   •  Managing  governance  and  organisa7onal  change  during  the   so3ware  lifecycle   •  Measuring  and  analysing  the  impact  of  so3ware  and  so3ware   processes   •  So3ware  aDribu7on,  cita7on,  and  credit   •  Interac7on  between  researchers,  developers  and  stakeholders   •  Transferable  so3ware  prac7ces  from  industry  
  • 7. Agenda  –  morning   Communi7es  and  Prac7ces   •  09:00  Introduc7on  to  the  Workshop   •  09:30  Sustainable  So3ware  for  Computa7onal  Chemistry          and  Materials  Modeling   •  10:00  Break   •  10:30  Adop7on  of  So3ware  by  a  User  Community:  The          Montage  Image  Mosaic  Engine  Example   •  11:00  On  Realizing  the  Concept  Study  ScienceSo3  of  the          European  Middleware  Ini7a7ve  -­‐  OpenSo3ware  for          Open  Science   •  11:30  The  Rela7onship  Between  Development  Problems          and  Use  of  So3ware  Engineering  Prac7ces  in          Computa7onal  Science   •  12:00  Lunch  
  • 8. Agenda  –  a3ernoon   Models  and  Methods   •  13:30  libHPC:  So3ware  sustainability  and  reuse          through  metadata  preserva7on   •  14:00  Overview  of  the  TriBITS  Lifecycle  Model   •  14:30  IPOL:  Reviewed  Publica7on  and  Public          Tes7ng  of  Research  So3ware          Debate  introduc7on   •  15:00  Break   •  15:30  Culture  Change  debate:  "What  can  we  do          to  change  the  status  quo?  Should  we  do  this?”   •  17:00  Close  
  • 9. Area  of  Interest  from  Audience   •  Prac7ces  and  models   •  Mixed  industry/academic  projects   •  Portability  across  heterogeneous   •  Integra7on  of  so3ware   plalorms   components   •  Ways  of  reducing  complexity   •  Sustaining  so3ware  on  liDle   •  Recording  informa7on  on   money   so3ware  structure   •  So3ware  engineering  applied  to   •  Making  so3ware  verifiable   computa7onal  science   •  Building  communi7es  around   •  Is  there  a  life  beyond  public   so3ware   funding  (e.g.  for  dCache)?   •  Cultural  issues  in  organisa7ons   •  So3ware  +  data  preserva7on  for   •  Collabora7on  between   10  years  usage  (e.g.  Tevatron)     ins7tu7ons  and  countries   •  Taking  responsibility  for  orphaned   •  Meta-­‐issues  of  so3ware  across   so3ware  (e.g.  for  OSG)   science  and  social  science   •  Understanding  what  so3ware’s   been  funded  and  what’s   happened  to  it?  
  • 10. Culture  Change  Discussion   •  Goals   –  Understand  what  are  the  key  barriers  to  culture   change  with  respect  to  so3ware  in  research   –  Understand  who  and  what  needs  to  change,  to   change  the  status  quo   –  Record  the  studies,  examples,  prac7ces  and   models  that  the  workshop  par7cipants  agree   should  be  highlighted  
  • 11. Ques7ons   1  What  are  the  basic  so3ware  skills  and   understanding  every  scien7st  needs?   –  Beverly  Sanders  et  al.   2  Life  beyond  public  grant  funding  –  what  happens   next?   –  Bruce  Berriman,  Michael  McLennan,  Jennifer  Schopf,   Nigel  Ward,  Jim  Willenbring   3  So3ware  reward,  cita7on,  aDribu7on.  Tracking   usage  and  impact   –  Neil  Chue  Hong,  Alberto  Di  Meglio,  Josh  Greenberg,   Juan  Lalinde,  Kevin  Jorissen  
  • 12. Process   •  Brainstorm  issues  and  ideas  (45  mins,  around  break)   –  Put  down  ideas  without  judgement  (it  doesn’t  maDer  if   someone  else  doesn’t  think  it’ll  work)   –  If  you’ve  heard  of  something,  write  it  down   •  Understand  and  group  (15  mins)   –  Do  you  have  the  same  understanding  of  all  the  ideas   –  Are  some  of  the  ideas  linked   •  Priori7se  and  record  (30  mins)   –  What  are  the  biggest  issues?   –  What  are  the  ideas  that  you’ve  seen  that  (don’t)  work  best?   –  Are  there  trends/correla7ons  that  should  be  explored?   •  Share  your  findings  (15  mins)   •  Please  record  digitally  so  that  it  can  be  easily  shared