FAIR DATA Fund use case: BioBrAIn – a database of bioreactors 

Authors: Héc­tor Mal­don­a­do de León, Vic­tor Puig I Labor­da, Mah­di Naderibeni and Cees Haringa  

Brief descrip­tion of the project 

Despite recent advances, Com­pu­ta­tion­al Flu­id Dynam­ics (CFD) sim­u­la­tions of biore­ac­tors remain com­pu­ta­tion­al­ly demand­ing, espe­cial­ly for assess­ing full bio­process­es or opti­miz­ing design. 

Reduced Order Mod­els (ROMs) offer a solu­tion, by reduc­ing the com­plex­i­ty of the mod­el while main­tain­ing spa­tial detail afford­ably. More­over, these mod­els allow for inte­grat­ing hydro­dy­nam­ics and bio­ki­net­ics at an afford­able cost.  

How­ev­er, the use of reduced order mod­els in biore­ac­tor analy­sis is hin­dered by the steep learn­ing curve of CFD soft­ware, time expense of cre­at­ing a CFD data­base, and lim­it­ed access to com­pre­hen­sive data­bas­es essen­tial for train­ing and test­ing these mod­els.  

Our project focus­es on open­ly release a data­base of well-doc­u­ment­ed CFD sim­u­la­tions to over­come these bar­ri­ers, thus facil­i­tat­ing rapid ROM devel­op­ment and enabling researchers to bench­mark and com­pare alter­na­tive dimen­sion­al­i­ty reduc­tion meth­ods. 

The data­base is called Bio­BrAIn (Biore­ac­tor Analy­sis and Intel­li­gence), and con­tains CFD sim­u­la­tions for three reac­tor geome­tries and sev­er­al oper­at­ing con­di­tions to democ­ra­tize access to essen­tial biore­ac­tor data. This allows sci­en­tists and engi­neers to ana­lyze bio­process­es more effi­cient­ly with­out requir­ing access to CFD and high-per­for­mance com­put­ing, facil­i­tat­ing devel­op­ments in mod­el and data-dri­ven bio­process design and opti­miza­tion. 

Bio­BrAIn is an ini­tia­tive from the CASE group at the Biotech­nol­o­gy Depart­ment of the Fac­ul­ty of Applied Sci­ences at TU Delft and col­leagues from the Tech­ni­cal Uni­ver­si­ty of Den­mark (DTU).  

Key results:  

• An open access data­base of well-doc­u­ment­ed CFD sim­u­la­tions of biore­ac­tors 

• A pro­pos­al for prop­er­ly doc­u­ment­ing CFD sim­u­la­tions in the biotech­nol­o­gy field 

How FAIR Data Fund is sup­port­ing the project:  

The FAIR Data Fund allowed us to hire a stu­dent assis­tant (Ansh Gup­ta, Chem­i­cal Engi­neer­ing MSc. Stu­dent) to cre­ate the man­u­al for inter­pret­ing and visu­al­iz­ing the data from the var­i­ous sim­u­la­tions at hand. Fur­ther­more, the 4TU.ResearchData team helped craft the doc­u­men­ta­tion of the datasets and host­ed the large datasets to be pub­licly avail­able.  

We are grate­ful to the team and 4TU.ResearchData for their sup­port in advanc­ing the devel­op­ment of sur­ro­gate mod­els for biore­ac­tors by mak­ing the data pub­licly avail­able.  

The col­lec­tion of data­bas­es is avail­able on the 4TU.ResearchData repos­i­to­ry.