Automated Metabolic P System Placement in FPGA

Kulakovskis, Darius; Navakauskas, Dalius

doi:10.1515/ecce-2016-0001

Cited by 3 publications

(2 citation statements)

References 20 publications

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“…While various attempts have been carried out and are currently ongoing to imitate membrane systems, some of these had been implemented on single-processor computers [13], neglecting the intrinsic parallelism of the systems being simulated. Efforts are now focused on increasing membrane-system simulation speed through the use of multicore processors [14][15][16][17], cluster of computers [10,18], designs of parallel hardware and the field programming gate arrays (FPGA) [19,20], and graphics processing units (GPU) [21][22][23][24][25][26]. Installation and employment of cluster computing are cost-prohibitive, making this option feasible only for large companies.…”

Section: Introductionmentioning

confidence: 99%

A Representation of Membrane Computing with a Clustering Algorithm on the Graphical Processing Unit

Muniyandi

Maroosi

2020

Processes

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Long-timescale simulations of biological processes such as photosynthesis or attempts to solve NP-hard problems such as traveling salesman, knapsack, Hamiltonian path, and satisfiability using membrane systems without appropriate parallelization can take hours or days. Graphics processing units (GPU) deliver an immensely parallel mechanism to compute general-purpose computations. Previous studies mapped one membrane to one thread block on GPU. This is disadvantageous given that when the quantity of objects for each membrane is small, the quantity of active thread will also be small, thereby decreasing performance. While each membrane is designated to one thread block, the communication between thread blocks is needed for executing the communication between membranes. Communication between thread blocks is a time-consuming process. Previous approaches have also not addressed the issue of GPU occupancy. This study presents a classification algorithm to manage dependent objects and membranes based on the communication rate associated with the defined weighted network and assign them to sub-matrices. Thus, dependent objects and membranes are allocated to the same threads and thread blocks, thereby decreasing communication between threads and thread blocks and allowing GPUs to maintain the highest occupancy possible. The experimental results indicate that for 48 objects per membrane, the algorithm facilitates a 93-fold increase in processing speed compared to a 1.6-fold increase with previous algorithms.

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Section: Introductionmentioning

confidence: 99%

A Representation of Membrane Computing with a Clustering Algorithm on the Graphical Processing Unit

Muniyandi

Maroosi

2020

Processes

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“…Instead, the aspect of photoinhibition is focused on. Non photochemical quenching (NPQ), another aspect of photosynthesis, has been modelled using a metabolic P system [18,22]. A probabilistic approach to photosynthesis interaction in cyanobacteria is described in [4,30].…”

Section: Introductionmentioning

confidence: 99%

Coping with dynamical reaction system topologies using deterministic P modules: a case study of photosynthesis

Hinze

2020

J Membr Comput

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The topology of chemical reaction networks is commonly treated as a static structure. This might be sufficient if substrate concentrations and kinetic parameter values exclusively determine the behaviour of all considered reactions. In contrast, numerous phenomena observed in life sciences imply a different nature by dynamical composition of reaction schemes. Single reactions or functional groups of reactions (modules) become activated or deactivated by external signals such as light intensity while the system is in operation. In other scenarios, reactions emerge or disappear while modules can connect to each other or disconnect due to presence or absence of corresponding trigger signals. We capture dynamical reaction network structures by an extended version of deterministic P modules with evaluation of trigger signals which facilitates detailed in-silico simulation studies and hence an easier understanding and prediction of complex biological systems. A case study dedicated to photosynthesis in plants demonstrates its usefulness beyond pure employment of ordinary differential equations by consideration of events, non-differentiable external trigger signals, and thresholds which collaterally modify the underlying reaction scheme.

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Intraveninio Gliukozės Tolerancijos Testo Metabolinės P Sistemos Įgyvendinimas Apibendrintuoju Kombinaciniu Būdu / Intravenous Glucose Tolerance Test Metabolic P System Implemented Using Unified Combinative Technique

Kulakovskis¹

2019

Science - Future of Lithuania

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Metabolic P (MP) systems are a part of the infobiotics research field. The intravenous glucose tolerance test (IVGTT) MP system models glucose-insulin interactions. MP system implementation in software is well researched, although there is a lack of techniques for hardware implementation, specifically with field programmable gate arrays. In this article the existing techniques are examined first, including combinative, single digital signal processor element, and pipelined. Then the specifics of six different IVGTT MP systems are analyzed. Having in mind these specifics, a new unified combinative IVGTT MP system implementation in field programmable gate arrays is proposed. Carried out experimental investigation results confirm, that the proposed unified system in comparison with single IVGTT MP systems, uses 36% less digital signal processor and 49% less look-up table resources of the field programmable gate arrays. Santrauka Metabolinė P (MP) sistema yra naujos infobiotikos mokslo srities dalis. Intraveninio gliukozės tolerancijos testo (IVGTT) MP sistema modeliuojama gliukozės ir insulino sąveika. MP sistemų įgyvendinimas programinėmis priemonėmis yra gerai ištirtas, tačiau trūksta MP sistemoms įgyvendinti aparatinėje įrangoje, konkrečiai – lauku programuojamose loginėse matricose (LPLM), skirtų metodų. Šiame straipsnyje iš pradžių aptariami taikytini žinomi įgyvendinimo būdai: kombinacinis, vieno skaitmeninio signalų apdorojimo elemento ir srautinis. Vėliau nagrinėjamos šešios skirtingos IVGTT MP sistemos ir nustatomi jų ypatumai. Atsižvelgiant į bendras IVGTT MP sistemų savybes, pasiūlomas naujas apibendrintas kombinacinis IVGTT MP sistemų įgyvendinimo būdas, kuris sujungia visas minėtas sistemas vienoje LPLM. Palyginus apibendrintą sistemą su atskiromis IVGTT MP sistemomis, nustatyta, kad apibendrinta sistema naudoja 36 % mažiau skaitmeninių signalų apdorojimo elementų ir 49 % mažiau peržvalgos lentelių visoms šešioms žinomoms IVGTT MP sistemoms apskaičiuoti.

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Automated Metabolic P System Placement in FPGA

Cited by 3 publications

References 20 publications

A Representation of Membrane Computing with a Clustering Algorithm on the Graphical Processing Unit

A Representation of Membrane Computing with a Clustering Algorithm on the Graphical Processing Unit

Coping with dynamical reaction system topologies using deterministic P modules: a case study of photosynthesis

Intraveninio Gliukozės Tolerancijos Testo Metabolinės P Sistemos Įgyvendinimas Apibendrintuoju Kombinaciniu Būdu / Intravenous Glucose Tolerance Test Metabolic P System Implemented Using Unified Combinative Technique

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