Sustaining a robust metabolic network requires a balanced and fully functioning proteome. In addition to amino acids, many enzymes require cofactors (coenzymes and engrafted prosthetic groups) to function properly. Extensively validated resource allocation models, such as genome-scale models of metabolism and gene expression (ME-models), have the ability to compute an optimal proteome composition underlying a metabolic phenotype, including the provision of all required cofactors. Here we apply the ME-model for Escherichia coli K-12 MG1655 to computationally examine how environmental conditions change the proteome and its accompanying cofactor usage. We found that: (1) The cofactor requirements computed by the ME-model mostly agree with the standard biomass objective function used in models of metabolism alone (M-models); (2) ME-model computations reveal non-intuitive variability in cofactor use under different growth conditions; (3) An analysis of ME-model predicted protein use in aerobic and anaerobic conditions suggests an enrichment in the use of peroxyl scavenging acids in the proteins used to sustain aerobic growth; (4) The ME-model could describe how limitation in key protein components affect the metabolic state of E. coli. Genome-scale models have thus reached a level of sophistication where they reveal intricate properties of functional proteomes and how they support different E. coli lifestyles.

This paper presents a novel method for finding frequent items in data streams using a homogeneous counter-based hardware array. The presented array is a close hardware adaptation of the well-known Space-Saving algorithm. The array can identify frequent items with frequencies larger than a specified threshold with a single pass through the input dataset. When implemented on an Intel Arria 10 FPGA, 40% of the FPGA resources are sufficient for 1000+ hardware counters. This is enough to guarantee the identification of all frequent items with frequency thresholds as low as 0.1% of the size of any dataset, regardless of the input distribution. Compared to other hardware implementations, the presented architecture is the fastest on average, and the first to retain the guarantee property of the Space-Saving algorithm on the reported frequent items. In addition, test results on synthetic and real datasets showed that the presented method can achieve more than 11x throughput speedup compared to software implementations of the algorithm and up to 50% better precision compared to other hardware implementations.

The unique capability of acetogens to ferment a broad range of substrates renders them ideal candidates for the biotechnological production of commodity chemicals. In particular the ability to grow with H2:CO2 or syngas (a mixture of H2/CO/CO2) makes these microorganisms ideal chassis for sustainable bioproduction. However, advanced design strategies for acetogens are currently hampered by incomplete knowledge about their physiology and our inability to accurately predict phenotypes. Here we describe the reconstruction of a novel genome-scale model of metabolism and macromolecular synthesis (ME-model) to gain new insights into the biology of the model acetogen Clostridium ljungdahlii. The model represents the first ME-model of a Gram-positive bacterium and captures all major central metabolic, amino acid, nucleotide, lipid, major cofactors, and vitamin synthesis pathways as well as pathways to synthesis RNA and protein molecules necessary to catalyze these reactions, thus significantly broadens the scope and predictability. Use of the model revealed how protein allocation and media composition influence metabolic pathways and energy conservation in acetogens and accurately predicted secretion of multiple fermentation products. Predicting overflow metabolism is of particular interest since it enables new design strategies, e.g. the formation of glycerol, a novel product for C. ljungdahlii, thus broadening the metabolic capability for this model microbe. Furthermore, prediction and experimental validation of changing secretion rates based on different metal availability opens the window into fermentation optimization and provides new knowledge about the proteome utilization and carbon flux in acetogens.

Genome-scale models of metabolism and macromolecular expression (ME-models) explicitly compute the optimal proteome composition of a growing cell. ME-models expand upon the well-established genome-scale models of metabolism (M-models), and they enable a new fundamental understanding of cellular growth. ME-models have increased predictive capabilities and accuracy due to their inclusion of the biosynthetic costs for the machinery of life, but they come with a significant increase in model size and complexity. This challenge results in models which are both difficult to compute and challenging to understand conceptually. As a result, ME-models exist for only two organisms (Escherichia coli and Thermotoga maritima) and are still used by relatively few researchers. To address these challenges, we have developed a new software framework called COBRAme for building and simulating ME-models. It is coded in Python and built on COBRApy, a popular platform for using M-models. COBRAme streamlines computation and analysis of ME-models. It provides tools to simplify constructing and editing ME-models to enable ME-model reconstructions for new organisms. We used COBRAme to reconstruct a condensed E. coli ME-model called iJL1678b-ME. This reformulated model gives functionally identical solutions to previous E. coli ME-models while using 1/6 the number of free variables and solving in less than 10 minutes, a marked improvement over the 6 hour solve time of previous ME-model formulations. Errors in previous ME-models were also corrected leading to 52 additional genes that must be expressed in iJL1678b-ME to grow aerobically in glucose minimal in silico media. This manuscript outlines the architecture of COBRAme and demonstrates how ME-models can be created, modified, and shared most efficiently using the new software framework.

BACKGROUND: Genome-scale models of metabolism and macromolecular expression (ME) significantly expand the scope and predictive capabilities of constraint-based modeling. ME models present considerable computational challenges: they are much (>30 times) larger than corresponding metabolic reconstructions (M models), are multiscale, and growth maximization is a nonlinear programming (NLP) problem, mainly due to macromolecule dilution constraints. RESULTS: Here, we address these computational challenges. We develop a fast and numerically reliable solution method for growth maximization in ME models using a quad-precision NLP solver (Quad MINOS). Our method was up to 45 % faster than binary search for six significant digits in growth rate. We also develop a fast, quad-precision flux variability analysis that is accelerated (up to 60× speedup) via solver warm-starts. Finally, we employ the tools developed to investigate growth-coupled succinate overproduction, accounting for proteome constraints. CONCLUSIONS: Just as genome-scale metabolic reconstructions have become an invaluable tool for computational and systems biologists, we anticipate that these fast and numerically reliable ME solution methods will accelerate the wide-spread adoption of ME models for researchers in these fields.

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)--in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.

This article presents a new solution for easing the development of reconfigurable applications using Field-Programable Gate Arrays (FPGAs). Namely, our Reliable Reconfigurable Real-Time Operating System (R3TOS) provides OS-like support for partially reconfigurable FPGAs. Unlike related works, R3TOS is founded on the basis of resource reusability and computation ephemerality. It makes intensive use of reconfiguration at very fine FPGA granularity, keeping the logic resources used only while performing computation and releasing them as soon as it is completed. To achieve this goal, R3TOS goes beyond the traditional approach of using reconfigurable slots with fixed boundaries interconnected by means of a static communication infrastructure. Instead, R3TOS approaches a static route-free system where nearly everything is reconfigurable. The tasks are concatenated to form a computation chain through which partial results naturally flow, and data are exchanged among remotely located tasks using FPGA’s reconfiguration mechanism or by means of “removable” routing circuits. In this article, we describe the R3TOS microkernel architecture as well as its hardware abstraction services and programming interface. Notably, the article presents a set of novel circuits and mechanisms to overcome the limitations and exploit the opportunities of Xilinx reconfigurable technology in the scope of hardware multitasking and dependability.

This paper presents a new technique to be used in the context of reconfigurable computing to accelerate the online diagnosis of permanent damage on Xilinx FPGAs using Built-In Self Tests (BISTs). Detecting and locating permanently damaged resources with precision is central to keep the system implemented on the FPGA flawless at all times; i.e. upcoming hardware tasks are mapped to available functional resources, circumventing the use of the damaged ones. The proposed diagnostic technique exploits the Multiple Frame Write (MFW) feature available in Xilinx FPGAs to “clone” (i.e. replicate) a single basic BIST circuit along arbitrarily sized and shaped areas on the FPGA without incurring large time overheads. Hence, the proposed technique allows for creating at runtime on-demand tailored BIST circuits to satisfy any diagnosis requirements that may rise up. Moreover, the proposed solution allows for saving memory in the system as it only requires storing basic BIST circuits. Finally, the paper presents a diagnostic service for a Reliable Reconfigurable Real-Time Operating System (R3TOS) that is based on the BIST cloning technique and works in cooperation with the R3TOS fault-handling and recovery mechanisms.

MOTIVATION: Genome-scale metabolic models have been used extensively to investigate alterations in cellular metabolism. The accuracy of these models to represent cellular metabolism in specific conditions has been improved by constraining the model with omics data sources. However, few practical methods for integrating metabolomics data with other omics data sources into genome-scale models of metabolism have been developed. RESULTS: GIM(3)E (Gene Inactivation Moderated by Metabolism, Metabolomics and Expression) is an algorithm that enables the development of condition-specific models based on an objective function, transcriptomics and cellular metabolomics data. GIM(3)E establishes metabolite use requirements with metabolomics data, uses model-paired transcriptomics data to find experimentally supported solutions and provides calculations of the turnover (production/consumption) flux of metabolites. GIM(3)E was used to investigate the effects of integrating additional omics datasets to create increasingly constrained solution spaces of Salmonella Typhimurium metabolism during growth in both rich and virulence media. This integration proved to be informative and resulted in a requirement of additional active reactions (12 in each case) or metabolites (26 or 29, respectively). The addition of constraints from transcriptomics also impacted the allowed solution space, and the cellular metabolites with turnover fluxes that were necessarily altered by the change in conditions increased from 118 to 271 of 1397. AVAILABILITY: GIM(3)E has been implemented in Python and requires a COBRApy 0.2.x. The algorithm and sample data described here are freely available at: http://opencobra.sourceforge.net/ CONTACTS: [email protected]

Despite the clear potential of FPGAs to push the current power wall beyond what is possible with general-purpose processors, as well as to meet ever more exigent reliability requirements, the lack of standard tools and interfaces to develop reconfigurable applications limits FPGAs' user base and makes their programming not productive. R3TOS is our contribution to tackle this problem. It provides systematic OS support for FPGAs, allowing the exploitation of some of the most advanced capabilities of FPGA technology by inexperienced users. What makes R3TOS special is its nonconventional way of exploiting on-chip resources: These are used indistinguishably for carrying out either computation or communication tasks at different times. Indeed, R3TOS does not rely on any static infrastructure apart from its own core circuitry, which is constrained to a specific region within the FPGA where it is implemented. Thus, the rest of the device is kept free of obstacles, with the spare resources ready to be used as and whenever needed. At runtime, the hardware tasks are scheduled and allocated with the dual objective of improving computation density and circumventing damaged resources on the FPGA.

This paper presents a novel hardware mechanism to facilitate the design and implementation of soft processors on FPGAs using the Error-correcting code (ECC)-protected memory and Triple Modular Redundancy (TMR). Such techniques highly harden the fault tolerance of soft processors, especially their memories, which are the most radiation susceptible resources on FPGAs. This is demonstrated in the implementation of a fault-tolerant PicoBlaze processor on Xilinx FPGAs, in which we used an additional LookAhead technique to synchronize the processor with ECC-protected Block RAM (ECC BRAM). The resulting fault-tolerant PicoBlaze processor has the benefit of having a self-recoverable program memory in the presence of Single Error Upsets (SEUs), without halting the processor. Our techniques can be applied to other soft processors e.g. Xilinx MicroBlaze or Altera Nios.