Motivation: Rapid advances in live-cell imaging analysis and mathematical modeling have produced a large amount of quantitative data on spatiotemporal dynamics of biological objects ranging from molecules to organisms. There is now a crucial need to bring these large amounts of quantitative biological dynamics data together centrally in a coherent and systematic manner. This will facilitate the reuse of this data for further analysis.Results: We have developed the Systems Science of Biological Dynamics database (SSBD) to store and share quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei and whole organisms in a wide variety of model organisms from Escherichia coli to Mus musculus. The data are provided in Biological Dynamics Markup Language format and also through a REST API. In addition, SSBD provides 188 sets of time-lapse microscopy images from which the quantitative data were obtained and software tools for data visualization and analysis.Availability and Implementation: SSBD is accessible at http://ssbd.qbic.riken.jp.Contact: sonami@riken.jp
AbsIrtwI-Titi paiper describes the Stnoker Makihinej ant niTite4Iuotnt robotic systern that iWis huu.i hotwettn hit 1985 irnid tarly 1988. Th prnjdc was documented by the BI(' ow the course of 2 Yk~I The Snhokr MAtbhtt" was broadcasted otn IIIC( territorial cltind iii the liK an tbe ott houir Q.YFI). science programmew of loth March 1988. IThis paper summaries tb technwica details of tUw systotn It cI%isteId6f vi%dul'o aSon AUu,v expert wsohm aiul As robot marnpUtl4to. It oujtlinies srniw of the difficnItites that the SnookQr Machine hAd to overcome~in pIaymng a gatne uf ulookeri11 JgAtift ai htirn anplayr.n Givetn the~recet in t m1rests an developing robotic %ysttuts to play po6dI2I, 13]; l4I; this; patpr hlQk ht at somue of those ksuuti. It 41o outhll(s soni coimputationatl ntlgitapprnoxch% hat "a cad su~hn or r(1 At the timnc automnated manufacturing was mainfly basedon prerogrtrimed iJ'leXihblc tuak wkiti fixed lcations Tbewhr~w-as a niced lur~intelligent robots catble QI sensiHg, muaking deiscions tni o r to hadleC rreg~ular compnen~uts and com1plex tasks The Stiboko Rohot Player Orc ciSJxas fir ci usiOned Atid kd by P of Koorosh K iodaha didcloo, Whli headedd the RuotA6L~And Ma uladuing Systems Rcardh (Grou At Bnixlti university. ne ft.ect was joined by Prof JRut BIldwin ad hi Al grou p at Bristol Th h deaI wa's to use Shookbr[lj, a game of pb I which wva very poplar in the UK to dec'n otaei tiei fundamentldrif)icipie of mrifIiciA inteligeceIL in fLbotiL. it was beieved t It the, ba i tchnloAgy fbr devel p1u i ueh an initlligui f6bo wxotidl bc iranstlirable td handle complex industrial tasks by~Ad ptiIng tO Atievr changing envi[onmftt Ati intJllge rit robo ukld he a r)obt which has to deAl wlith 'unrtiauy 11 sens ng t s informa~tion ciit th tiran Adadptiju to ph7lyscal rosrctions oi r ft wn lrim~itation efth&rtrIot gh itg own knowldgc ba-s o thrFough xexh ft efiviroumntc 11 PRf)II(. ORJECIVES\AND SYrim REitI REMEN\rs I hic,Ihflfl~'hamctcisticA or requirementuc of ti Intlign I ) The system u ist operate. ato finialy matking dcciii rwh the iic 6f scnsorv data Ah ratc1lt~ige r6bot mits be able to search h r Alternative slutotis' in case 2) D)ata is uathetrcd u\mng seisrs anid k owledge 'is up-Aninmtellign t' btic str hoti yk~Ild be ablc to d&aI wAith un certi itiatJo U a dfd cwnflitig informaion.) It hotild be Abl to deriv a possble soltion or to asu lu frther set f actions in orOrd to resolve thec situaJI OnU Oci oft de mina objectives of thic project was to) pus the iYonimcr Qf uditieliet robtic systems and to demonstrat that sut i a systen~i cotld. [e trainsferred and be use it in dutr~iali apolications. It was tici decided tha equipmn it an software packages used (or te prqIOc had tk be1 oite-shif, T4ulorĩ ade solutions w~e kcpt to a muninu mi Ilhk oIther maii ob tvewa ti explor an~d to moddl uncer Ul l( c~taiiyimrcs deinitions vague human concepts atid statis in hwunan decisin rnaki Kg~througi 1h ga u O snoOk r Snooker woul1d gfve Al researchcrs a swgrnicant number ol' chaiull i dcalin~'W itkh~lc cpc tati...
Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats.Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis.Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/.Contact: sonami@riken.jpSupplementary Information: Supplementary data are available at Bioinformatics online.
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