Three-dimensional graphical reconstruction from HVEM stereoviews of biological specimens by means of a microcomputer

A microcomputer reconstruction technique has been developed in order to permit a larger exploitation of stereomicroscopy. The microcomputer facility consists of a digitizing tablet, a microcomputer, a graphics terminal, a graphics plotter and a printer. The technique has been applied to the study of HVEM stereopairs, performed by recording two images of the same area of a specimen (thick section of araldite-embedded leech ganglion neurons), tilted relative to the beam axis through an angle 0/20 degrees. Coordinates of N conjugate points of interest, expressed in a common reference system were obtained with the help of a digitizing tablet and the misorientation between the two images was determined by a method based on a least square technique. New projections of the object on different planes are provided by the microcomputer facility. Also the microcomputer method permits to obtain new stereopairs drawings, in various orientations and slices from a three-dimensional reconstruction of the object oriented in any direction in space. The method permits to obtain computed anaglyph drawings, printed here, which are stereoviews of the same object.     

Microcomputer analysis of hyperbolic and non-hyperbolic steady-state kinetics

A BASIC computer program has been developed which has been used to show that bovine lens aldose reductase with NADPH as substrate follows a 1:1 function, while rabbit lens hexokinase has a rate equation of minimum degree 2:2, and bovine lens polyol dehydrogenase has a rate equation of minimum degree 1:2 with xylitol as substrate. The parameter estimates obtained are very close to those from the BMDP3R curvefitting program on an ICL 2980 mainframe computer, with identical conclusions as to the minimum degree of the rate equation. The computer program can be run on any microcomputer with high resolution graphics in less than 48 K of random access memory.     

A comprehensive system of cosinor treatment programs written for the Apple II microcomputer

A comprehensive set of cosinor treatment programs has been written for an Apple II microcomputer. The system includes Single Cosinor, Mean (population) Cosinor and Serial Sections analyses as well as extensive graphics and file management. The package is integrated and used through a hierarchically ordered system of menus and choices. 48k memory and two disk drives are required, and both EPSON and SILENTYPE printers are supported.     

A CAL program to teach the basic principles of genetic engineering—a change from the traditional approach

An interactive computer-assisted learning program written for the BBC microcomputer to teach the basic principles of genetic engineering is described. The pro-gram makes extensive use of colour, graphics, and animation and is aimed at A-level students of biology. Students select, from a menu, to investigate one of a number of identified processes involved in the overall production of a protein, each of which is treated as a self-contained unit. An assessment of how much of the factual information the student has learned is provided in the form of a computer 'adventure game' which is not only challenging but fun to play. Briefly, the student is led into an imaginary laboratory and must choose from shelves those essential items (e.g. reagents, starting materials, techniques) to progress through several stages culminating in the production of genetically engineered bacteria capable of producing a specific protein.     

Computerized continuous monitoring of cytochemical enzyme reaction product formation by the Vickers M85A microdensitometer

Summary An experimental set-up for the continuous monitoring of cytochemical enzyme reaction rates is described. The design consists of a 32K Commodore PET microcomputer, upgraded to Basic 4 and containing a graphics facility. The microcomputer is interfaced with a Vickers M85A microdensitometer, which has been modified and equipped with a Zeiss X63 water immersion objective. The software allows for the automatic transfer of density readings from the M85A to the microcomputer, and for the continuous monitoring of the enzyme reaction as its proceeds at short time intervals (i.e. down to 3.3 s). The relationship between the absorbance change of the enzyme final reaction product and time is printed both numerically and graphically. Initial velocity rates are calculated by regression analysis, and statistical evaluation of grouped data is possible.     

Real-time three-dimensional graphic reconstructions using Brown-Roberts-Wells frame coordinates in a microcomputer environment

A desktop microcomputer environment that utilizes Brown-Roberts-Wells (BRW) frame coordinates for creation of three-dimensional depiction of operator-defined intracranial structures has been developed. The system allows direct reading of Siemens CT scan images from a floppy disc, structural edge definition, and reconstruction of defined images. The system is used in the operating room to view scans, perform standard BRW stereotactic functions, and create three-dimensional graphics for such tasks as defining tumor margins, conceptualizing positional relationships of intracranial structures, and radiation planning.     

Graphical representations of the class I MHC cleft

We describe computer graphics and computer aided manufacture of three-dimensional models designed specifically to elucidate the cleft in the class I human leukocyte antigen. The models evolve from computer graphical representations and provide a geometrically and chemically concise and detailed view of the antigen binding site. The techniques provide a new approach to representations of binding sites. The model provides sufficient detail to support binding specificities analysis of active sites involved in protein and DNA binding.     

江豚耳蜗切片的计算机三维重建

在自己组装的微型机图象系统上,实现了对生物组织连续切片的三维重建。重建结果以灰度阴影方式在彩色显示器上显示,并可在打印机上以多灰度等级方式打印输出。结合一例江豚内耳的连续切片,对其耳蜗骨迷路部份进行了三维重建。并将重建结果以动态形式在显示器上转动,以便观察其各个侧面的情况。     

From Static to Interactive: Transforming Data Visualization to Improve Transparency

Data presentation for scientific publications in small sample size studies has not changed substantially in decades. It relies on static figures and tables that may not provide sufficient information for critical evaluation, particularly of the results from small sample size studies. Interactive graphics have the potential to transform scientific publications from static reports of experiments into interactive datasets. We designed an interactive line graph that demonstrates how dynamic alternatives to static graphics for small sample size studies allow for additional exploration of empirical datasets. This simple, free, web-based tool (http://statistika.mfub.bg.ac.rs/interactive-graph/) demonstrates the overall concept and may promote widespread use of interactive graphics.     

New programs: XELE—a polypeptide model-building program for a graphics workstation

A model-building program, XELE, for use in protein crystallography has been written in C under UNIX on a graphics workstation. This program makes full use of the X Window system to display the electron density distribution and to manipulate the polypeptide model, and therefore is named XELE. It utilizes a fast three-dimensional rendering package, Dorè, and is portable to other types of graphics workstations. A part of the program for the man-machine interface uses the library of X Window and X Toolkit, and therefore is highly interactive. The structure analysis program package, PROTEIN, is also implemented in an interactive mode using X Window, and has been interfaced with XELE.     

Prediction of the conformation and antigenic determinants of the V-sis viral oncogene product homologous with human platelet-derived growth factor

In an extensive study involving unification of secondary structure prediction methods to predict peptide backbone angles, folding simulations, and interactive graphics we have calculated conformations for a 160 residue p28sis protein fragment. We demonstrate that the state of the art is sufficient to aid artificial vaccine design.     

ANTHEPROT: a package for protein sequence analysis using a microcomputer

A simple microcomputer package is described to make the theoreticalanalysis of protein sequences. Several methods designed to comparetwo sequences, to model proteolytic reactions and to predictthe secondary structure, the hydro-phobic/hydrophilic regionsand the potential antigenic sites of proteins have been includedin an Apple II microcomputer software. The package comprises21 programs as well as the secondary structure database of Kabschand Sander (1983). Received on November 24, 1987; accepted on March 8, 1988     

Annotating PDB files with scene information

We have implemented extensions to the Brookhaven Protein Data Bank (PDB) file format for incorporating scene information such as viewing parameters, additional molecular information (e.g., van der Waals radii and atom colors), and user-defined graphics. These extensions were made in conformance with the PDB standard and provide sufficient information to render the scene in various styles such as space-filling images and ribbon diagrams. For the past 5 years these extensions have been used in the MidasPlus molecular modeling system and have proved both powerful and sufficient for generating complex molecular images. We propose that the extensions to the PDB presented here be adopted by the molecular modeling community for incorporation into visualization programs.     

Display of three-parametric data acquired by a flow cytometer

A program for producing contour maps of three-parameter flow cytometric data is described. The program is written in Pascal and can be implemented on any microcomputer with a graphics screen.     

录象机在生物组织连续切片的计算机三维重建系统中的应用

录象机(Video Tape Recorder)作为输入、输出设备,应用于“生物组织连续切片的计算机三维重建系统”中,其效果是令人满意的.由于研制的“同步再生”单元(Sync RecoveryUnit)有效地消除了静放噪声,从而使Cromemco微型计算机的图象输入接口SDD(Super DazzlerDigitizer)能够稳定地逐帧采集录象机输出的静止图象.录制并编辑计算机三维重建后的生物组织显微结构的空间旋转视图,使其在录象机的监视器上显示得更生动、逼真,更有体视感;还可脱离主机在任何场合演示重建结果.本文还就录象机在生物医学序列图象分析中的应用前景进行了讨论.     

Generating precise mechanical stimuli and recording chordotonal organ discharge patterns using a microcomputer

A computer-controlled system for the investigation of the responseproperties of the tibio-femoral chordotonal organ in the locustis described. The computer is used to generate small amplitudesinusoidal movements of the tibia via a small servo-controlledmotor. The resulting response recorded via a suction electrodeis simultaneously detected, processed and stored on disk. Fullconstructional details for all hardware required are given.The software, developed for a BBC microcomputer, in additionto controlling all the hardware, has graphics and analysis routinesenabling the operator to display and manipulate the stored data.     

GCWIND: a microcomputer program for identifying open reading frames according to codon positional G + C content

GCWIND is a microcomputer (IBM-PC compatible) program for theidentification of protein-coding open reading frames. The programis similar to the FRAME program, but the latter has only beenimplemented for a specialized graphics package. The base compositions(%G+C)for each of the three possible reading phases throughthe DNA sequence are displayed separately, together with thepositions of potential translation initiation and terminationcodons (on the leading and complementary strands), to providean immediate representation of those regions within the sequencethat have coding potential.     

Enhancement and simplification of macromolecular images.

Computer graphics programs have been devised to display selected atomic features and to simplify images of complex macromolecular structures. By using boundary outlines, adjustment of size and shape of the molecular components, color coding, shading, and selective omission of obscuring detail, attention can be focused on specific interactions which determine higher levels of organization. A balanced color table has been constructed in which different hues have equal steps in brightness; this table has facilitated distinction of atom types and sequence coding together with representation of an optimum range of depth cueing and surface shading. The graphics system has been used with the atomic coordinates of the tobacco mosaic virus structure to simplify images of the protein subunit, to illustrate intermolecular interactions, and to relate subunit packing arrangements in different assemblies to the underlying atomic structure. The system has also been used to construct a schematic representation of the polyomavirus capsid, based on low resolution data. Application of artistic methods contributes to the effective presentation and interpretation of detailed scientific information about complex macromolecular structures.     

A microcomputer program for hydropathic analysis of proteins with I/O through word processing and graphics software

A BASIC program has been devised for the hydropathic analysisof protein sequences according to the method of Kyte and Doolittle(1982). The program uses sequence data from input files thatare created with a word processor and produces two types ofoutput file: one contains a bar graph of the hydropathic profilein a format that can be easily edited; the other is a tabulationof hydropathic indices along a protein's sequence that can beused as input by the program for the production of a bar graphor as input into other graphics and analysis software. An MS-DOSmicrocomputer, operating under IBM BASICA or GWBASIC and a dotmatrix printer with block graphics capabilities are the onlyhardware requirements for graphic display of hydropathy profiles.The program is capable of unattended analysis from a list ofup to 15 input files. ; accepted on March 10, 1986     

PCDRA: PC interactive molecular representation and modeling system

PCDRA was designed to provide the average biologist with a user-friendly molecular display on a low-cost personal computer. The package is menu driven and is built so that a biologist, with tittle or no computing knowledge, finds it easy to use. The system gives a color representation with depth cueing of a protein whose atomic coordinates are stored as a PDB file. Moreover, the system presents several features similar to HYDRA¹ and therefore is a good introduction to molecular graphics, especially for beginners in protein modeling.