Darwin v. 2.0: an interpreted computer language for the biosciences

MOTIVATION: We announce the availability of the second release of Darwin v. 2.0, an interpreted computer language especially tailored to researchers in the biosciences. The system is a general tool applicable to a wide range of problems. RESULTS: This second release improves Darwin version 1.6 in several ways: it now contains (1) a larger set of libraries touching most of the classical problems from computational biology (pairwise alignment, all versus all alignments, tree construction, multiple sequence alignment), (2) an expanded set of general purpose algorithms (search algorithms for discrete problems, matrix decomposition routines, complex/long integer arithmetic operations), (3) an improved language with a cleaner syntax, (4) better on-line help, and (5) a number of fixes to user-reported bugs. AVAILABILITY: Darwin is made available for most operating systems free of char ge from the Computational Biochemistry Research Group (CBRG), reachable at http://chrg.inf.ethz.ch. CONTACT: darwin@inf.ethz.ch     

Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language

Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.     

Simulating flow microfluorometry experiments with the computer language cellsim

CELLSIM is a digital simulation language specifically designed for simulating cell kinetics models. Recently a flow microfluorometry (FMF) command has been added to the language. In the command, the modeler indicates when his simulated FMF analyses are to take place, and what cell states are to be included. He may specify different coefficients of variance and a non-linear DNA synthesis rate for S phase cells. The FMF capability of the language has proved to be a useful tool in several applications.     

Teaching human genetics in biochemistry by computer literature searching.

We describe a new user-intense-learning experience that incorporates the teaching of clinical and research applications of human genetics in biochemistry while training first-year medical students to develop skills in computer access to the literature. Human genetics was incorporated into the biochemistry curriculum by providing each student with experience in on-line literature searching in MEDLINE, using Grateful Med, in order to write an abstract about a specific inherited biochemical disorder. We stressed the need for the students to obtain current information in order to understand and interpret the rapidly changing field of human genetics. We taught the students that the most efficient method of obtaining such information was by searching the medical literature via computer.     

Exploring virtual environments with an EEG-based BCI through motor imagery.

In this paper, we describe the possibility of navigating in a virtual environment using the output signal of an EEG-based Brain-Computer Interface (BCI). The graphical capabilities of virtual reality (VR) should help to create new BCI-paradigms and improve feedback presentation. The objective of this combination is to enhance the subject's learning process of gaining control of the BCI. In this study, the participant had to imagine left or right hand movements while exploring a virtual conference room. By imaging a left hand movement the subject turned virtually to the left inside the room and with right hand imagery to the right. In fact, three trained subjects reached 80% to 100% BCI classification accuracy in the course of the experimental sessions. All subjects were able to achieve a rotation in the VR to the left or right by approximately 45 degrees during one trial.     

PAL: an object-oriented programming library for molecular evolution and phylogenetics.

Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers. AVAILIABILTY: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License.     

Surgical instruments and dressings: an information service.

A regional information service on surgical equipment, instruments, and dressings is proposed that would be staffed by information scientists. It would appreciably reduce the time spent on administration and make the buying of equipment more efficient. Such a service could be extended to all health service staff.     

计算机虚拟筛选技术在害虫行为调节剂研究中的应用

害虫行为调节剂是一种以嗅觉系统为靶标的绿色农药,在害虫的田间管理中发挥着重要的作用。然而,其先导化合物的发现通常依赖一系列生物测定的方法,不仅费时费力,且发现效率低。近年来,随着昆虫嗅觉功能数据的积累和结构生物学的飞速发展,以机器学习技术和分子对接为代表的2种基于计算机的药物虚拟筛选方法在害虫行为调节剂的先导化合物研究中发挥着重要的作用,极大地促进了先导化合物的发现效率,减少了筛选的盲目性。本文系统综述了2种虚拟筛选方法及其在害虫行为调节剂先导化合物研究中的应用,并对2种筛选策略在实际应用中存在的问题及应用前景进行了讨论。     

Redesigning, implementing and integrating Escherichia coli genome software tools with an object-oriented database system

This paper reports our exploratory work to redesign, implementand integrate a collection of genome software tools with anobject-oriented database system. Our software tools deal withgenome data from Escherichia coli K-12, a bacterium that hasbeen studied intensively and provides richer data sets thanany other living organism. The object-oriented DBMS used forthe integration is ONTOS, a commercial object-oriented systemfrom Ontologic Inc. This redesign and implementation task wasperformed in two steps. First, Cprograms were converted intoC+ +, and then the C+ + version programs were modified and integratedwith an object-oriented modeling of the data to form an ONTOSdatabase application. The first step helps us develop a conceptualview for a DBMS-independent object-oriented construct. The secondstep elucidates what additional DBMS-dependent modificationsteps are needed to provide persistency to the objects. Examplesare included to illustrate steps of the redesign and implementation.Overall, the outcome of this project demonstrates that programsand data can be successfully integrated with an object-orienteddatabase, while providing the objects with persistency and shareability.This paper includes discussions using concrete examples on whatadvantage the object–oriented database approach providesover the relational database approach.     

Waves of states in an electron beam with a distributed virtual cathode

Results are presented from computer simulations of the dynamics of an electron beam injected into the drift space between two parallel conducting planes. The specific features of the competitive coexistence of states with and without a virtual cathode are investigated.     

Fluorometric detection of deoxyribonucleic acid synthesis; possibilities for interfacing bromodeoxyuridine dye techniques with flow fluorometry.

Fluorometric detection of the biosynthetic incorporation of 5-bromodeoxyuridine (BrdU) into deoxyribonucleic acid has permitted cytologic studies of chromosome structure, replication, and repair. Some of these phenomena, previously detected using BrdU-dye techniques on fixed microscopic preparations, should be particularly amenable to analogous experimentation in fluorescence flow systems. Problems involved in interfacing BrdU-dye methodology with flow fluorometry are discussed. The effects of certain chemical modifications of bisbenzimidazole dyes on their spectroscopic properties and potential use for detecting BrdU incorporation into unfixed cells are described. Data on the use and energy transfer characteristics of a pair of deoxyribonucleic acid-binding dyes (33258 Hoechst and ethidium bromide) capable of simultaneously providing information about BrdU substitution and total deoxyribonucleic acid content are presented.