Published Modelling Biology – working through (in-)stabilities and frictions

Just had our paper on Com­pu­ta­tion­al Biol­o­gy pub­lished in the online jour­nal Com­pu­ta­tion­al Cul­ture.
Alex S. Tay­lor, Jas­min Fish­er, Byron Cook, Samin Ish­ti­aq and Nir Piter­man (2014) Mod­el­ling Biol­o­gy – work­ing through (in-)stabilities and fric­tions. Com­pu­ta­tion­al Cul­ture, 1 (4).

Abstract: Com­pu­ta­tion­al biol­o­gy is a nascent field reliant on soft­ware cod­ing and mod­el­ling to pro­duce insights into bio­log­i­cal phe­nom­e­na. Extreme claims cast it as a field set to replace con­ven­tion­al forms of exper­i­men­tal biol­o­gy, see­ing soft­ware mod­el­ling as a (more con­ve­nient) proxy for bench-work in the wet-lab. In this arti­cle, we deep­en and com­pli­cate the rela­tions between com­pu­ta­tion and sci­en­tif­ic ways of know­ing by dis­cussing a com­pu­ta­tion­al biol­o­gy tool, BMA, that mod­els gene reg­u­la­to­ry net­works. We detail the insta­bil­i­ties and fric­tions that sur­face when com­pu­ta­tion is incor­po­rat­ed into sci­en­tif­ic prac­tice, fram­ing the ten­sions as part of knowing-in-progress—the prac­ti­cal back and forth in work­ing things out. The work exem­pli­fies how soft­ware studies—and care­ful atten­tion to the mate­ri­al­i­ties of computation—can shed light on the emerg­ing sci­ences that rely on cod­ing and com­pu­ta­tion. Fur­ther, it puts to work a stand­point that sees com­pu­ta­tion as tight­ly entan­gled with forms of sci­en­tif­ic know­ing and doing, rather than a whole­sale replace­ment of them.