MOLKERN: A library of software components for molecular modeling programs

The library of software components MOLKERN is designed to construct efficient programs (with linear computational complexity) for modeling, optimization, and analysis of spatial structures of proteins, cofactors, ligands, and their complexes and computation of their physical properties. The interactions between atoms and molecules are taken into account within the force field method. The library is realized in C++ using static polymorphism technology. The library utilizes STL and BOOST libraries and contains a number of software components for parallel computation using the MPI technology. The library can be used under Windows and Linux.

     

A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at http://www.math.unipa.it/~raffaele/BATS/ under the GNU GPL.     

Developing a Model Driven Approach for engineering applications based on mOSAIC

In many scientific and engineering areas there are emerging software services available over the Web. The reason for deploying such services in the Cloud is either to reduce the operational costs or to support the peaks in their usage profiles. The algorithms employed in such services are usually result of a long term research and technology development work, so it is beneficial to reuse those critical application parts when developing new Cloud applications. This paper investigates the possibilities to introduce a Model Driven Architecture (MDA) for the Cloud computing domain, which would support composition, customization, flexibility, maintenance and reusability of Cloud application components in the particular case of scientific and engineering applications. The underlying middleware technology of choice is the mOSAIC Platform as a Service (PaaS) solution. This choice is motivated by the fact that in mOSAIC a Cloud application consists of loosely coupled components, which are either generic and provide for key resource types needed by an application (computation, storage, communication) or custom made, e.g. based on existing legacy software. The MDA approach is illustrated through the design and operation of an application for analysis of structures under static loading. It is shown that a relatively simple design can be used to address two application bottlenecks: the varying number of users and the computational complexity of the given problem. The design reduces the necessary application development efforts and the key components can be reused for similar applications.     

The Bioinformatics Template Library--generic components for biocomputing

MOTIVATION: The efficiency of bioinformatics programmers can be greatly increased through the provision of ready-made software components that can be rapidly combined, with additional bespoke components where necessary, to create finished programs. The new standard for C++ includes an efficient and easy to use library of generic algorithms and data-structures, designed to facilitate low-level component programming. The extension of this library to include functionality that is specifically useful in compute-intensive tasks in bioinformatics and molecular modelling could provide an effective standard for the design of reusable software components within the biocomputing community. RESULTS: A novel application of generic programming techniques in the form of a library of C++ components called the Bioinformatics Template Library (BTL) is presented. This library will facilitate the rapid development of efficient programs by providing efficient code for many algorithms and data-structures that are commonly used in biocomputing, in a generic form that allows them to be flexibly combined with application specific object-oriented class libraries. AVAILABILITY: The BTL is available free of charge from our web site http://www.cryst.bbk.ac.uk/~classlib/ and the EMBL file server http://www.embl-ebi.ac.uk/FTP/index.html     

A modular software concept for individual numerical simulation (FEM) of the human mandible]

A new modular software concept for individual numerical simulation of the human mandible using the finite element method (FEM) is presented. The main task is an individual analysis of regional stress and stress-compatibility on the basis of computed tomographic data in individual patients. Simulation should, however, also be possible in parallel with biomechanical experiments, or for further research projects. For this purpose, rapid and uncomplicated generation of the FEM model, easy modification of input data, and short computation times are required. Practical use in the clinical setting makes appreciable additional demands on the individual software components.     

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.     

Oscillatory Threshold Logic

In the 1940s, the first generation of modern computers used vacuum tube oscillators as their principle components, however, with the development of the transistor, such oscillator based computers quickly became obsolete. As the demand for faster and lower power computers continues, transistors are themselves approaching their theoretical limit and emerging technologies must eventually supersede them. With the development of optical oscillators and Josephson junction technology, we are again presented with the possibility of using oscillators as the basic components of computers, and it is possible that the next generation of computers will be composed almost entirely of oscillatory devices. Here, we demonstrate how coupled threshold oscillators may be used to perform binary logic in a manner entirely consistent with modern computer architectures. We describe a variety of computational circuitry and demonstrate working oscillator models of both computation and memory.     

Secure outsourcing of modular exponentiations in cloud and cluster computing

Cloud computing and cluster computing are user-centric computing services. The shared software and hardware resources and information can be provided to the computers and other equipments according to the demands of users. A majority of services are deployed through outsourcing. Outsourcing computation allows resource-constrained clients to outsource their complex computation workloads to a powerful server which is rich of computation resources. Modular exponentiation is one of the most complex computations in public key based cryptographic schemes. It is useful to reduce the computation cost of the clients by using outsourcing computation. In this paper, we propose a novel outsourcing algorithm for modular exponentiation based on the new mathematical division under the setting of two non-colluding cloud servers. The base and the power of the outsourced data can be kept private and the efficiency is improved compared with former works.     

Open-Source 3D-Printable Optics Equipment

Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods.     

"Glyco-peakfinder"--de novo composition analysis of glycoconjugates

Mass spectrometric techniques are the key technology for rapid and reliable glycan analysis. However, the lack of robust, dependable, and freely available software for the (semi-) automatic annotation of mass spectra is still a severe bottleneck that hampers their rapid interpretation. In this article the "Glyco-Peakfinder" web-service is described allowing de novo determination of glycan compositions from their mass signals. Starting from a basic set of mandatory masses of glycan components, the calculation can be performed without any knowledge concerning the biological background of the sample or the fragmentation technique used. "Glyco-Peakfinder" assigns all types of fragment ions including monosaccharide cross-ring cleavage products and multiply charged ions. It provides full user control to handle modified glycans (persubstituted molecules, reducing-end modifications, glycoconjugates) and ion types. The formula applied to calculate the fragment masses and an outline of the implemented algorithm are discussed. A systematic evaluation of the dependence of all factors influencing the computation time revealed strikingly different impact of the individual calculation steps. To provide access to known carbohydrate structures a "composition search" in the open access database GLYCOSCIENCES.de can be performed. The service is available at the URL: www.eurocarbdb.org/applications/ms-tools.     

Power efficient virtual machine placement in cloud data centers with a discrete and chaotic hybrid optimization algorithm

Cluster Computing - Cloud computing is a new computation technology that provides services to consumers and businesses. The main idea of Cloud computing is to present software and hardware services...     

噬菌体抗体库技术在肿瘤抗体药物研究中的进展及应用

目的:综述噬菌体抗体库技术的研究进展,介绍该技术的原理,构建,筛选和应用,为抗肿瘤抗体药物研发提供参考。方法:采用文献综述的方法,筛选近5年来噬菌体抗体库技术试验论文,对噬菌体抗体库技术的原理,构建,筛选和应用进行总结。结果:噬菌体抗体库主要分为免疫抗体库和非免疫抗体库两大类;噬菌体抗体库筛选技术包括亲和筛选、细胞筛选和生物体内筛选三种;噬菌体抗体库技术主要应用于肿瘤标志物的识别和肿瘤诊断,抗肿瘤抗体药物的筛选和制备。结论:噬菌体抗体库技术方便、快速、高效,可以在体外环境下培养,这些特点决定了其在肿瘤标志物的发现和肿瘤抗体药物研发中的广泛应用。目前噬菌体抗体库技术还存在一定缺陷,但技术的不断发展和革新必然使噬菌体抗体库技术成为研制抗体药物的新思路,极大促进了肿瘤抗体药物的研发。     

Isolation of Functional RNA from Periderm Tissue of Potato Tubers and Sweet Potato Storage Roots

A reliable and efficient protocol is given for the isolation of mRNA from the periderm of potato tubers and sweet potato storage roots. The method relies on a urea-based lysis buffer and lithium chloride to concentrate total RNA away from most of the cytoplasmic components and to prevent oxidation of phenolic complexes. To enhance the physical separation of the RNA from other macromolecular components, the RNA fraction was incubated in the presence of the cationic surfactant Catrimox-14. Poly(A)⁺ mRNA was separated from total RNA and other contaminants by using Promega's MagneSphere technology. The mRNA was suitable for cDNA library construction and RNA fingerprinting.     

The animat: new frontiers in whole brain modeling

The researchers at Boston University (BU)'s Neuromorphics Laboratory, part of the National Science Foundation (NSF)-sponsored Center of Excellence for Learning in Education, Science, and Technology (CELEST), are working in collaboration with the engineers and scientists at Hewlett-Packard (HP) to implement neural models of intelligent processes for the next generation of dense, low-power, computer hardware that will use memristive technology to bring data closer to the processor where computation occurs. The HP and BU teams are jointly designing an optimal infrastructure, simulation, and software platform to build an artificial brain. The resulting Cog Ex Machina (Cog) software platform has been successfully used to implement a large-scale, multicomponent brain system that is able to simulate some key rat behavioral results in a virtual environment and has been applied to control robotic platforms as they learn to interact with their environment.     

SeqCor: correct the effect of guide RNA sequences in clustered regularly interspaced short palindromic repeats/Cas9 screening by machine learning algorithm

Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based screening using various guide RNA (gRNA) libraries has been executed to identify functional components for a wide range of phenotypes with regard to numerous cell types and organisms. Using data from public CRISPR/Cas9-based screening experiments, we found that the sequences of gRNAs in the library influence CRISPR/Cas9-based screening. As building a standard strategy for correcting results of all gRNA libraries is impractical, we developed SeqCor, an open-source programming bundle that enables researchers to address the result bias potentially triggered by the composition of gRNA sequences via the organization of gRNA in the library used in CRISPR/Cas9-based screening. Furthermore, SeqCor completely computerizes the extraction of sequence features that may influence single-guide RNA knockout efficiency using a machine learning approach. Taken together, we have developed a software program bundle that ought to be beneficial to the CRISPR/Cas9-based screening platform.     

Marathon: An Open Source Software Library for the Analysis of Markov-Chain Monte Carlo Algorithms

We present the software library marathon, which is designed to support the analysis of sampling algorithms that are based on the Markov-Chain Monte Carlo principle. The main application of this library is the computation of properties of so-called state graphs, which represent the structure of Markov chains. We demonstrate applications and the usefulness of marathon by investigating the quality of several bounding methods on four well-known Markov chains for sampling perfect matchings and bipartite graphs. In a set of experiments, we compute the total mixing time and several of its bounds for a large number of input instances. We find that the upper bound gained by the famous canonical path method is often several magnitudes larger than the total mixing time and deteriorates with growing input size. In contrast, the spectral bound is found to be a precise approximation of the total mixing time.     

Libsequence: a C++ class library for evolutionary genetic analysis

A C++ class library is available to facilitate the implementation of software for genomics and sequence polymorphism analysis. The library implements methods for data manipulation and the calculation of several statistics commonly used to analyze SNP data. The object-oriented design of the library is intended to be extensible, allowing users to design custom classes for their own needs. In addition, routines are provided to process samples generated by a widely used coalescent simulation. AVAILABILITY: The source code (in C++) is available from http://www.molpopgen.org     

DNA library design for molecular computation.

A novel approach to designing a DNA library for molecular computation is presented. The method is employed for encoding binary information in DNA molecules. It aims to achieve a practical discrimination between perfectly matched DNA oligomers and those with mismatches in a large pool of different molecules. The approach takes into account the ability of DNA strands to hybridize in complex structures like hairpins, internal loops, or bulge loops and computes the stability of the hybrids formed based on thermodynamic data. A dynamic programming algorithm is applied to calculate the partition function for the ensemble of structures, which play a role in the hybridization reaction. The applicability of the method is demonstrated by the design of a twelve-bit DNA library. The library is constructed and experimentally tested using molecular biology tools. The results show a high level of specific hybridization achieved for all library words under identical conditions. The method is also applicable for the design of primers for PCR, DNA sequences for isothermal amplification reactions, and capture probes in DNA-chip arrays. The library could be applied for integrated DNA computing of twelve-bit instances of NP-complete combinatorial problems by multi-step DNA selection in microflow reactors.