Computer programs for nucleic acid sequence manipulation

Computer programs are described which help during the collection and analysis of nucleic acid sequence data. They are written in FORTRAN and have been implemented on a PDP 11/60 computer.     

NEUREC - a program package for 3D-reconstruction from serial sections using a microcomputer

A software package is described to reconstruct three-dimensional pictures in true perspective from a series of parallel sections using a low-cost computer system (Apple II plus). Data sampling via a graphic tablet and graphical output on the monitor screen or a digital plotter are assigned to different programs under control of a menu program. The number of data representing the object under study is unlimited. Originally written in BASIC, the programs were translated to machine language. As an application of the package, reconstructions of an identified large interneuron of the locust brain are presented.     

Recovery of penicillin by reactive extraction in centrifugal extractors

Penicillin V and/or G were extracted from fermentation broth by Amberlite LA-2 in n-butylacetate at pH 5 in a laboratory centrifugal extractor, Type SA 01 of Westfalia, up to an overall phase throughput rate of 30 L/h, in a bench-scale four-stage extraction system, consisting of Type TA 1 of Westfalia, up to an overall phase throughput rate of 110 L/h, and in a pilot-plant three-stage extraction unit, consisting of Type TA 7 extractors of Westfalia, up to a phase throughput rate of 990 L/h with very high degrees of extraction (up to 99%). The reextraction from the ion-pair complex, which contained organic solvent, was performed by phosphate, borate, or carbonate buffer at pH 7.5-8.5 in all three extractor systems with degrees of extraction up to 98%, but at considerably lower overall phase throughput rates than those of the extraction, since no satisfactory phase separation is possible at higher throughput rates.     

EEG data acquisition and preprocessing by microcomputer satellite system

Recent development in computer technology allows already medium scale EEG data processing to be performed within the clinical neurophysiology department, if a fast minicomputer with adequate mass storage and graphical output facilities is used. Data acquisition, however, should be delegated to a microcomputer which also should take over as much preprocessing as possible. A system is presented, where one or several microcomputer-based satellite units perform analog-digital conversion, Fourier transformation (FFT), calculation of power spectra and crossproducts, as well as event related averaging or other preprocessing procedures. The units are connected to a fast central minicomputer, where a supervisor program loads the microprocessors with their programs, supervises their activity, receives preprocessed data and activates appropriate postprocessing programs to produce the final results.     

A visual data flow environment for macromolecular crystallographic computing

This article describes the integration of programs from the widely used CCP4 macromolecular crystallography package into a modern data flow visualization environment (application visualization system [AVS]), which provides a simple graphical user interface, a visual programming paradigm, and a variety of 1-, 2-, and 3-D data visualization tools for the display of graphical information and the results of crystallographic calculations, such as electron density and Patterson maps. The CCP4 suite comprises a number of separate Fortran 77 programs, which communicate via common file formats. Each program is encapsulated into an AVS macro module, and may be linked to others in a data flow network, reflecting the nature of many crystallo-graphic calculations. Named pipes are used to pass input parameters from a graphical user interface to the program module, and also to intercept line printer output, which can be filtered to extract graphical information and significant numerical parameters. These may be passed to downstream modules, permitting calculations to be automated if no user interaction is required, or giving the user the opportunity to make selections in an interactive manner.     

A quantitative method for the analysis of cell shape and locomotion

A rapid, semiautomated system to quantitate and analyze leukocyte shape and locomotion was developed. Video images of moving leukocytes were obtained using a Vidicon camera mounted on a Nikon phase microscope. The video signal was either inputted directly, or indirectly via a video cassette recorder, to a Datacube video analog-digital, digital-analog converter. A Digital Equipment Corporation LSI 11/23 computer using the RT-11/TSX-Plus operating system and computer programs written in FORTRAN and MARCO assembly language permitted image segmentation, image display, and calculation of position, speed, direction of movement and orientation of each leukocyte at 10 s intervals. These data were stored on a winchester disk for subsequent evaluation of the leukocyte orientation, speed and direction of movement using statistical and graphical methods. The reproducibility of measurements made with the video system was tested by comparison with manual measurements; a correlation coefficient of 0.998 was obtained for the two methods. Rates of chemokinesis were then determined for unstimulated and chemokinetically stimulated polymorphonuclear leukocytes (PMNs) and found to average 12.8 micron/min and 18.1 micron/min, respectively. The high speed, ease of data analysis, and potential for multiparameter evaluation makes this system useful for directly evaluating leukocyte locomotion.     

Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds

ABSTRACT: BACKGROUND: The MapReduce framework enables a scalable processing and analyzing of large datasets by distributing the computational load on connected computer nodes, referred to as a cluster. In Bioinformatics, MapReduce has already been adopted to various case scenarios such as mapping next generation sequencing data to a reference genome, finding SNPs from short read data or matching strings in genotype files. Nevertheless, tasks like installing and maintaining MapReduce on a cluster system, importing data into its distributed file system or executing MapReduce programs require advanced knowledge in computer science and could thus prevent scientists from usage of currently available and useful software solutions. RESULTS: Here we present Cloudgene, a freely available platform to improve the usability of MapReduce programs in Bioinformatics by providing a graphical user interface for the execution, the import and export of data and the reproducibility of workflows on in-house (private clouds) and rented clusters (public clouds). The aim of Cloudgene is to build a standardized graphical execution environment for currently available and future MapReduce programs, which can all be integrated by using its plug-in interface. Since Cloudgene can be executed on private clusters, sensitive datasets can be kept in house at all time and data transfer times are therefore minimized. CONCLUSIONS: Our results show that MapReduce programs can be integrated into Cloudgene with little effort and without adding any computational overhead to existing programs. This platform gives developers the opportunity to focus on the actual implementation task and provides scientists a platform with the aim to hide the complexity of MapReduce. In addition to MapReduce programs, Cloudgene can also be used to launch predefined systems (e.g. Cloud BioLinux, RStudio) in public clouds. Currently, five different bioinformatic programs using MapReduce and two systems are integrated and have been successfully deployed. Cloudgene is freely available at http://cloudgene.uibk.ac.at.     

A simulation support system for solving large physiological models on microcomputers

Although physiological modeling and computer simulation have become useful research tools to test new scientific theories and to design and analyze laboratory experiments, developing a new model can be a tedious process because the investigator must often write very complex and specific routines for data input and output. To facilitate the design of new models (as well as the use of existing models), we have developed MODSIM, a FORTRAN-based simulation support system for the IBM PC computer than can accommodate very large dynamic models having up to several thousand equations. It provides the investigator with utilities for continuous on-line graphical and/or tubular output, as well as facilities for dynamic interaction with the model. The user must only supply a model as a list of mathematical equations written in FORTRAN, along with the initial values of the model variables and parameters. The model is precompiled, compiled, and then linked to the MODSIM utilities. Without further programming, the user can then solve the model, select variables for graphical output, and stop the model at any time to analyze the data or to change a parameter before resuming the simulation. This simulation system makes it very easy to develop new models that actively interact with the experimental research of the investigator.     

Effects of speciation on partitioning of iodine in aqueous biphasic systems and onto ABEC resins

Polyethylene glycol (PEG)-aqueous biphasic systems (ABS) and PEG-grafted aqueous biphasic extraction chromatographic (ABEC) resins have been shown to remove inorganic species from environmental and nuclear wastes. The partitioning behavior of several iodide species (iodide, iodine, triiodide, iodate, and 4-iodo-2,6-dimethylphenol (I-DMP)) have been studied for PEG (MW 2000)-salt systems and ABEC resins. Iodide partitioning to PEG-rich phases or onto ABEC resins can be enhanced by derivatization with 2,6-dimethylphenol to form 4-iodo-2,6-dimethylphenol or by addition of I(2) to form triiodide. Conversely, iodide partitioning to the PEG-rich phase or onto ABEC resins is reduced by oxidation of iodide to IO(3)(-). Partitioning studies of iodide, iodate, and iodine in a PEG-ABS are compared to results using ABEC resins.     

Bosque: integrated phylogenetic analysis software

Phylogenetic analyses today involve dealing with computer files in different formats and often several computer programs. Although some widely used applications have integrated important functionalities for such analyses, they still work with local resources only: input/output files (users have to manage them) and local computing (users have sometimes to leave their programs, on their desktop computers, running for extended periods of time). To address these problems we have developed 'Bosque', a multi-platform client-server software that performs standard phylogenetic tasks either locally or remotely on servers, and integrates the results on a local relational database. Bosque performs sequence alignments and graphical visualization and editing of trees, thus providing a powerful environment that integrates all the steps of phylogenetic analyses. AVAILABILITY: http://bosque.udec.cl     

A quantitative method for the analysis of cell shape and locomotion

Summary A rapid, semiautomated system to quantitate and analyze leukocyte shape and locomotion was developed. Video images of moving leukocytes were obtained using a Vidicon camera mounted on a Nikon phase microscope. The video signal was either inputted directly, or indirectly via a video cassette recorder, to a Datacube video analog-digital, digital-analog converter. A Digital Equipment Corporation LSI 11/23 computer using the RT-11/TSX-Plus operating system and computer programs written in FORTRAN and MARCO assembly language permitted image segmentation, image display, and calculation of position, speed, direction of movement and orientation of each leukocyte at 10 s intervals. These data were stored on a winchester disk for subsequent evaluation of the leukocyte orientation, speed and direction of movement using statistical and graphical methods. The reproducibility of measurements made with the video system was tested by comparison with manual measurements; a correlation coefficient of 0.998 was obtained for the two methods. Rates of chemokinesis were then determined for unstimulated and chemokinetically stimulated polymorphonuclear leukocytes (PMNs) and found to average 12.8 m/min and 18.1 m/min, respectively. The high speed, ease of data analysis, and potential for multiparameter evaluation makes this system useful for directly evaluating leukocyte locomotion.In honour of Prof. P. van Duijn     

Real-time fuzzy-knowledge-based control of Baker's yeast production

A real-time fuzzy-knowledge-based system for fault diagnosis and control of bioprocesses was constructed using the object-oriented programming environment Small-talk/V Mac. The basic system was implemented in a Macintosh Quadra 900 computer and built to function connected on line to the process computer. Fuzzy logic was employed in handling uncertainties both in the knowledge and in measurements. The fuzzy sets defined for the process variables could be changed on-line according to process dynamics. Process knowledge was implemented in a graphical two-level hierachical knowledge base. In on-line process control the system first recognizes the current process phase on the basis of top-level rules in the knowledge-base. Then, according to the results of process diagnosis based on measurement data, the appropriate control strategy is subsequently inferred making use of the lower level rules describing the process during the phase in question. (c) 1995 John Wiley & Sons, Inc.     

Application of linear system analysis to the horizontal vestibulo-ocular reflex of the alert rhesus monkey using pseudorandom binary sequence and single frequency sinusoidal stimulation

Horizontal eye movements of the alert rhesus monkey resulting from both pseudorandom binary sequence (PRBS) and single frequency sinusoidal rotational stimulation were analyzed using a PDP 11/40 computer in order to generate gain, phase, and coherence estimates at discrete frequencies between 0.008 and 1.28 Hz. A computer simulation of vestibular induced eye movements was used to validate our analysis procedures and to determine the effects of digital noise. Frequency domain transfer functions derived from gain and phase estimates revealed that the responses to PRBS stimulation and to single frequency sinusoids were not appreciably different. PRBS testing was accomplished in approximately one third the time required for sinusoidal testing and yielded highly reproducible data. We conclude that PRBS stimulation is a reliable and efficient method for assessing linear system parameters of the horizontal vestibulo-ocular reflex. PRBS testing may be particularly and advantageous in studies of vestibulo-oculomotor plasticity in which rapid assessment of alterations in system dynamics is essential.     

Accessible high-throughput virtual screening molecular docking software for students and educators

We survey low cost high-throughput virtual screening (HTVS) computer programs for instructors who wish to demonstrate molecular docking in their courses. Since HTVS programs are a useful adjunct to the time consuming and expensive wet bench experiments necessary to discover new drug therapies, the topic of molecular docking is core to the instruction of biochemistry and molecular biology. The availability of HTVS programs coupled with decreasing costs and advances in computer hardware have made computational approaches to drug discovery possible at institutional and non-profit budgets. This paper focuses on HTVS programs with graphical user interfaces (GUIs) that use either DOCK or AutoDock for the prediction of DockoMatic, PyRx, DockingServer, and MOLA since their utility has been proven by the research community, they are free or affordable, and the programs operate on a range of computer platforms.     

A computer-assisted cell identification system

A computer and optical microscope image processing system for the acquisition, editing and analysis of quantitative, multivariate, cell nuclear data is described. The experimental equipment and methods are discussed, the mathematics used are presented, and the additions, modifications and deletions to the TICAS 11/45 set of computer programs for the analysis of the data are outlined.     

An automated laboratory control system: collection and analysis of behavioral and electro-physiological data.

A system of man-machine interactive PDP-11 assembly language programs is described which presents stimuli to a subject and records and analyzes behavioral and evoked potential data. The system was designed for researchers with no knowledge of computer programming and enables the user to create complicated sequences of stimulus presentations ("trials") and sequences of successive trials ("runs"), with no new programming required. The system is written for DEC.s DECLAB 11/40 system.     

Relationship between tumour resistance and the in vitro and in vivo cytotoxicity elicited by Salmonella antigens in immunized mice

Immunization of mice with the attenuated 11RX strain of Salmonella enteritidis (11RX) induces resistance to intraperitoneal (i.p.) tumour growth. Tumour resistance is much greater and lasts for a longer time following i.p. immunization than following intravenous (i.v.) immunization. This paper extends our previous observations that, after this resistance is lost, it can be recalled by a T cell-mediated reaction to an antigenic extract of the bacteria (11RX antigen) which is not protective in unimmunized mice. The duration of this sensitization to 11RX antigen was determined in mice immunized i.p. or i.v. with live 11RX by challenging them at various times after immunization with 131I (or 125I)-labelled Ehrlich ascites tumour (EAT) cells alone or mixed with 11RX antigen. In vivo killing of EAT cells was assayed by monitoring whole-body retention of radioactivity and this was correlated in the same mice with suppression of tumour growth and survival of the mice. The resistance recalled by 11RX antigen was short-lived and in vivo cytotoxic activity had subsided by 6 days after antigen injection. 11RX antigen also recalled the ability of the peritoneal cells to lyse 51Cr-labelled EAT cells in vitro and a close correlation was found between this activity and the cytotoxicity measured in vivo. The adherence properties of the cytotoxic cells and their inhibition by trypan blue indicated that they were macrophages.     

A user-friendly biological workstation

Learning methods developed by artificial intelligence research teams are very efficient for biological sequences analysis but they need running on large computers accessed by terminals. These computers are interfaced with standard displays involving long and unpleasant alphanumerical data handling. The "biological work station" is a personal computer with a color graphic screen providing a user-friendly interface for the artificial intelligence learning programs running on large computers. It provides to biologist a graphical convenient tool for sequence analysis built with efficient man-machine communication methods such as multiwindows, icons and mouse selection. It allows the biologist to edit and display sequences in an efficient and natural way, showing off directly on color pictures the data and the results of learning programs.