The Embryonics Project: a machine made of artificial cells.

It is possible to trace the origins of biological inspiration in the design of electronic circuits to the very dawn of the field of computer engineering, with the work of John von Neumann in the 1940s. To his brilliance we owe not only the first methodical attempts to define the electronic equivalents of many fundamental biological process, but also the development of the first self-replicating computing machines. Unfortunately, the electronic technology of the time would not allow a physical realization of von Neumann's machines, and it was not until the introduction of new programmable circuits in the 1980s that the field of bio-inspired machines gained new momentum. In this article, we describe the Embryonics (embryonic electronics) Project, an attempt to draw inspiration from the ontogenetic processes that determine the growth of multicellular organisms in the design of new, massively parallel arrays of processors (the artificial cells). Our cells are simple processors, all based on an identical hardware structure and all containing the same program (our artificial genome), but executing different parts of the genome depending on their spatial coordinates within the array. As in living beings, the presence of the genome in every cell allows the introduction of features such as self-replication and self-repair (cicatrization). In addition, the cells are implemented using an array of programmable elements (the artificial molecules), which allows their structure to be adapted to a given application. Through the parallel operation of many of these simple processors, we hope to realize highly complex systems, the equivalent of multicellular organisms in the natural world.     

GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops

ABSTRACT: BACKGROUND: Accurate and efficient RNA secondary structure prediction remains an important open problem in computational molecular biology. Historically, advances in computing technology have enabled faster and more accurate RNA secondary structure predictions. Previous parallelized prediction programs achieved significant improvements in runtime, but their implementations were not portable from niche high-performance computers or easily accessible to most RNA researchers. With the increasing prevalence of multi-core desktop machines, a new parallel prediction program is needed to take full advantage of today's computing technology. FINDINGS: We present here the first implementation of RNA secondary structure prediction by thermodynamic optimization for modern multi-core computers. We show that GTfold predicts secondary structure in less time than UNAfold and RNAfold, without sacrificing accuracy, on machines with four or more cores. CONCLUSIONS: GTfold supports advances in RNA structural biology by reducing the timescales for secondary structure prediction. The difference will be particularly valuable to researchers working with lengthy RNA sequences, such as RNA viral genomes.     

Experience with collaborating managers: node group manager and provisioning manager

This paper presents an autonomic system in which two managers with different responsibilities collaborate to achieve an overall objective within a cluster of server computers. The first, a node group manager, uses modeling and optimization algorithms to allocate server processes and individual requests among a set of server machines grouped into node groups, and also estimates its ability to fulfill its service-level objectives as a function of the number of server machines available in each node group. The second, a provisioning manager, consumes these estimates from one or more node group managers, and uses them to allocate machines to node groups over a longer timescale. We describe the operation of both managers and the information that flows between them, and present the results of some experiments demonstrating the effectiveness of our technique. Furthermore, we relate our architecture to a general autonomic computing architecture based on self-managing resources and patterns of inter-resource collaboration, and to emerging standards in the area of distributed manageability. We also discuss some of the issues involved in incorporating our implementation into existing products in the short term, and describe a number of further directions for this research.     

Membrane computing: brief introduction, recent results and applications

The internal organization and functioning of living cells, as well as their cooperation in tissues and higher order structures, can be a rich source of inspiration for computer science, not fully exploited at the present date. Membrane computing is an answer to this challenge, well developed at the theoretical (mathematical and computability theory) level, already having several applications (via usual computers), but without having yet a bio-lab implementation. After briefly discussing some general issues related to natural computing, this paper provides an informal introduction to membrane computing, focused on the main ideas, the main classes of results and of applications. Then, three recent achievements, of three different types, are briefly presented, with emphasis on the usefulness of membrane computing as a framework for devising models of interest for biological and medical research.     

POEtic: an electronic tissue for bio-inspired cellular applications

In this paper, we introduce the general architecture of a new electronic tissue called POEtic. This reconfigurable circuit is designed to ease the implementation of bio-inspired systems that bring cellular applications into play. It contains special features that allow a developer to realize systems that require evolution (Phylogenesis), development (Ontogenesis), and/or learning (Epigenesis). A dynamic routing algorithm has been added to a structure similar to that of common commercial FPGAs, in order to allow the creation of data paths between cells. As the creation of these paths is dynamic, it is possible to add new cells or to repair faulty ones at runtime.     

Virtualizing high-end GPGPUs on ARM clusters for the next generation of high performance cloud computing

High performance cloud computing is behind the scene powering “the next big thing” as the mainstream accelerator for innovation in many areas. We describe here how to accelerate inexpensive ARM-based computing nodes with high-end GPGPUs hosted on x86_64 machines using the GVirtuS general-purpose virtualization service. We draw the vision of a possible next generation computing clusters characterized by highly heterogeneous parallelism heading to a lower electric power demanding, less heat producing and more environmental friendliness. Preliminary but promising performance data suggest that this solution could be considered as part of the foundations of the next generation of high performance cloud computing components.     

Support vector machine classification and validation of cancer tissue samples using microarray expression data

MOTIVATION: DNA microarray experiments generating thousands of gene expression measurements, are being used to gather information from tissue and cell samples regarding gene expression differences that will be useful in diagnosing disease. We have developed a new method to analyse this kind of data using support vector machines (SVMs). This analysis consists of both classification of the tissue samples, and an exploration of the data for mis-labeled or questionable tissue results. RESULTS: We demonstrate the method in detail on samples consisting of ovarian cancer tissues, normal ovarian tissues, and other normal tissues. The dataset consists of expression experiment results for 97,802 cDNAs for each tissue. As a result of computational analysis, a tissue sample is discovered and confirmed to be wrongly labeled. Upon correction of this mistake and the removal of an outlier, perfect classification of tissues is achieved, but not with high confidence. We identify and analyse a subset of genes from the ovarian dataset whose expression is highly differentiated between the types of tissues. To show robustness of the SVM method, two previously published datasets from other types of tissues or cells are analysed. The results are comparable to those previously obtained. We show that other machine learning methods also perform comparably to the SVM on many of those datasets. AVAILABILITY: The SVM software is available at http://www.cs. columbia.edu/ approximately bgrundy/svm.     

The Gift from Nature： Bio-Inspired Strategy for Developing Innovative Bridges

Biology has been a brilliant teacher and a precious textbook to man-made construction for thousands of years, because it allows one to learn and be inspired by nature＇s remarkable and efficient structural systems. However, the emerging biomimetic studies have been of increasing interest for civil engineering design only in the past two decades. Bridge design is one of aspects on structural engineering of biomimeties that offers an enormous potential for inspiration in various aspects, such as the ge- ometry, structure, mechanism, energy use and the intelligence. Recently built bridges and design proposals in which biological systems have produced a range of inspiration are reviewed in this paper. Multidisciplinary cooperation is discussed for the implementation of bio-inspired methods in future design. A case study about using bio-inspired strategy is trying to present a problem-solving approach, yet further cooperation is still needed to utilize biomimetie studies for design inspiration. This paper aims to call a close multidisciplinary collaboration that promotes engineers to build more sustainable and smart structural systems for bridges in the 21 st century.     

Intra- and inter-individual genetic differences in gene expression

Genetic variation is known to influence the amount of mRNA produced by a gene. Because molecular machines control mRNA levels of multiple genes, we expect genetic variation in components of these machines would influence multiple genes in a similar fashion. We show that this assumption is correct by using correlation of mRNA levels measured from multiple tissues in mouse strain panels to detect shared genetic influences. These correlating groups of genes (CGGs) have collective properties that on average account for 52–79% of the variability of their constituent genes and can contain genes that encode functionally related proteins. We show that the genetic influences are essentially tissue-specific and, consequently, the same genetic variations in one animal may upregulate a CGG in one tissue but downregulate the CGG in a second tissue. We further show similarly paradoxical behaviour of CGGs within the same tissues of different individuals. Thus, this class of genetic variation can result in complex inter- and intraindividual differences. This will create substantial challenges in humans, where multiple tissues are not readily available. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. M. J. Cowley, C. J. Cotsapas, and R. B. H. Williams contributed equally to this work.     

Thermomechanical analysis of soft-tissue thermotherapy

Soft-tissue thermotherapy based on sub-ablative heating of collagenous tissues finds wide-spread application in medicine such as tissue welding, thermokeratoplasty, skin resurfacing, elimination of discogenic pain in the spine and treatment of joint instability. In this paper, heat-induced thermomechanical response characteristics of collagenous tissues are quantified by means of in vitro experimentation with a representative model tissue (New Zealand white rabbit patellar tendon). Three distinct heat-induced thermomechanical response regimes (defined by the rate of deformation and the variation of material properties) are identified. Arrhenius damage integral representation of collagenous tissue thermal history is shown to be adequate in establishing the master response curves for quantification of thermomechanical response for modeling purposes. The trade-off between the improved kinematical stability and compromised mechanical stability of the heated collagenous tissue is shown to be the major challenge hindering the success of subablative thermotherapies.     

Synthetic biology and its alternatives. Descartes,Kant and the idea of engineering biological machines

The engineering-based approach of synthetic biology is characterized by an assumption that ‘engineering by design’ enables the construction of ‘living machines’. These ‘machines’, as biological machines, are expected to display certain properties of life, such as adapting to changing environments and acting in a situated way. This paper proposes that a tension exists between the expectations placed on biological artefacts and the notion of producing such systems by means of engineering; this tension makes it seem implausible that biological systems, especially those with properties characteristic of living beings, can in fact be produced using the specific methods of engineering. We do not claim that engineering techniques have nothing to contribute to the biotechnological construction of biological artefacts. However, drawing on Descartes’s and Kant’s thinking on the relationship between the organism and the machine, we show that it is considerably more plausible to assume that distinctively biological artefacts emerge within a paradigm different from the paradigm of the Cartesian machine that underlies the engineering approach. We close by calling for increased attention to be paid to approaches within molecular biology and chemistry that rest on conceptions different from those of synthetic biology’s engineering paradigm.     

Coding and traceability for cells,tissues and organs for transplantation

Modern transplantation of cells, tissues and organs has been practiced within the last century achieving both life saving and enhancing results. Associated risks have been recognized including infectious disease transmission, malignancy, immune mediated disease and graft failure. This has resulted in establishment of government regulation, professional standard setting and establishment of vigilance and surveillance systems for early detection and prevention and to improve patient safety. The increased transportation of grafts across national boundaries has made traceability difficult and sometimes impossible. Experience during the first Gulf War with miss-identification of blood units coming from multiple countries without standardized coding and labeling has led international organizations to develop standardized nomenclature and coding for blood. Following this example, cell therapy and tissue transplant practitioners have also moved to standardization of coding systems. Establishment of an international coding system has progressed rapidly and implementation for blood has demonstrated multiple advantages. WHO has held two global consultations on human cells and tissues for transplantation, which recognized the global circulation of cells and tissues and growing commercialization and the need for means of coding to identify tissues and cells used in transplantation, are essential for full traceability. There is currently a wide diversity in the identification and coding of tissue and cell products. For tissues, with a few exceptions, product terminology has not been standardized even at the national level. Progress has been made in blood and cell therapies with a slow and steady trend towards implementation of the international code ISBT 128. Across all fields, there are now 3,700 licensed facilities in 66 countries. Efforts are necessary to encourage the introduction of a standardized international coding system for donation identification numbers, such as ISBT 128, for all donated biologic products.     

The parallelization of SPIDER on distributed-memory computers using MPI

We describe the strategies and implementation details we employed to parallelize the SPIDER software package on distributed-memory parallel computers using the message passing interface (MPI). The MPI-enabled SPIDER preserves the interactive command line and batch interface used in the sequential version of SPIDER, thus does not require users to modify their existing batch programs. We show the excellent performance of the MPI-enabled SPIDER when it is used to perform multi-reference alignment and 3-D reconstruction operations on a number of different computing platforms. We point out some performance issues when the MPI-enabled SPIDER is used for a complete 3-D projection matching refinement run, and propose several ways to further improve the parallel performance of SPIDER on distributed-memory machines.     

Training mechanical engineering students to utilize biological inspiration during product development

The use of bio-inspiration for the development of new products and devices requires new educational tools for students consisting of appropriate design and manufacturing technologies, as well as curriculum. At the University of Maryland, new educational tools have been developed that introduce bio-inspired product realization to undergraduate mechanical engineering students. These tools include the development of a bio-inspired design repository, a concurrent fabrication and assembly manufacturing technology, a series of undergraduate curriculum modules and a new senior elective in the bio-inspired robotics area. This paper first presents an overview of the two new design and manufacturing technologies that enable students to realize bio-inspired products, and describes how these technologies are integrated into the undergraduate educational experience. Then, the undergraduate curriculum modules are presented, which provide students with the fundamental design and manufacturing principles needed to support bio-inspired product and device development. Finally, an elective bio-inspired robotics project course is present, which provides undergraduates with the opportunity to demonstrate the application of the knowledge acquired through the curriculum modules in their senior year using the new design and manufacturing technologies.     

State transitions by molecules

In our previous paper, we described a method by which a state machine is implemented by a single-stranded DNA molecule whose 3'-end sequence encodes the current state of the machine. Successive state transitions are performed in such a way that the current state is annealed onto an appropriate portion of DNA encoding the transition table of the state machine and the next state is copied to the 3'-end by extension with polymerase. In this paper, we first show that combined with parallel overlap assembly, a single series of successive transitions can solve NP-complete problems. This means that the number of necessary laboratory steps is independent from the problem size. We then report the results of two experiments concerning the implementation of our method. One is on isothermal reactions which greatly increase the efficiency of state transitions compared with reactions controlled by thermal cycles. The other is on the use of unnatural bases for avoiding out-of-frame annealing. The latter result can also be applied to many DNA-based computing paradigms.     

BIOCOMPUTATION: Some history and prospects

At first glance, biology and computer science are diametrically opposed sciences. Biology deals with carbon based life forms shaped by evolution and natural selection. Computer Science deals with electronic machines designed by engineers and guided by mathematical algorithms. In this brief paper, we review biologically inspired computing. We discuss several models of computation which have arisen from various biological studies. We show what these have in common, and conjecture how biology can still suggest answers and models for the next generation of computing problems. We discuss computation and argue that these biologically inspired models do not extend the theoretical limits on computation. We suggest that, in practice, biological models may give more succinct representations of various problems, and we mention a few cases in which biological models have proved useful. We also discuss the reciprocal impact of computer science on biology and cite a few significant contributions to biological science.     

Machine Sharing in Manufacturing Systems: Total Flexibility versus Chaining

In this paper, we compare the operational performance of two machine-sharing configurations: total flexibility and chaining. We show that chaining captures most of the benefits of total flexibility while limiting the number of part types processed on any individual machine to only two. We examine the relative desirability of the two configurations under varying buffer sizes, loading conditions, number of machines, and setup times, as well as for different control policies. For nonzero setups times, we show that chained configurations can outperform fully flexible ones. This particularly is the case when either the number of machines or length of setup times is high. We also find that the effect of the system size on performance diminishes with the number of machines. This means that multiple smaller chains can perform almost as well as a single long one. Our results are consistent with the recent findings of Jordan and Graves (1995), who examined the economic benefits of chaining relative to full flexibility.     

The impact of the International Atomic Energy Agency (IAEA) program on radiation and tissue banking in Cuba

The first multi-tissue bank was founded at Havana in 1958. At that time, freeze-drying was used at the bank as a method of preserving, as well as Cobalt 60 irradiation to sterilise bone tissue, heart valves and others. The impact of the IAEA program in tissue banking activities in Cuba can be summarised as follows: (a) Increase in the production of sterilised tissues using ionising radiation (bone, pig skin and amnion) for medical treatment in the tissue bank of the Hospital Frank Pais; (b) increase of the quality of the productions of bone tissues, pig skin and amnion; (c) reduction in the import of tissues by increasing the local production of tissues; (d) sustainability in the number of donors through the implementation of a public and professional awareness campaign; (e) training of six persons in the Regional Training Centre of Buenos Aires; (f) qualification of one person in the administration of a tissue bank and in the implementation of a Quality System. The amount of tissues produced and sterilised using the ionising radiation techniques in the established banks was 25,510 units. The amount of patients treated with sterilised tissues produced by the established banks was 2,448.     

Effective and efficient data sampling using bitmap indices

With growing computational capabilities of parallel machines, scientific simulations are being performed at finer spatial and temporal scales, leading to a data explosion. The growing sizes are making it extremely hard to store, manage, disseminate, analyze, and visualize these datasets, especially as neither the memory capacity of parallel machines, memory access speeds, nor disk bandwidths are increasing at the same rate as the computing power. Sampling can be an effective technique to address the above challenges, but it is extremely important to ensure that dataset characteristics are preserved, and the loss of accuracy is within acceptable levels. In this paper, we address the data explosion problems by developing a novel sampling approach, and implementing it in a flexible system that supports server-side sampling and data subsetting. We observe that to allow subsetting over scientific datasets, data repositories are likely to use an indexing technique. Among these techniques, we see that bitmap indexing can not only effectively support subsetting over scientific datasets, but can also help create samples that preserve both value and spatial distributions over scientific datasets. We have developed algorithms for using bitmap indices to sample datasets. We have also shown how only a small amount of additional metadata stored with bitvectors can help assess loss of accuracy with a particular subsampling level. Some of the other properties of this novel approach include: (1) sampling can be flexibly applied to a subset of the original dataset, which may be specified using a value-based and/or a dimension-based subsetting predicate, and (2) no data reorganization is needed, once bitmap indices have been generated. We have extensively evaluated our method with different types of datasets and applications, and demonstrated the effectiveness of our approach.