Comparison of different approaches and computer programs for progress curve analysis of enzyme kinetics

For the analysis of enzyme kinetics, a variety of programs exists. These programs apply either algebraic or dynamic parameter estimation, requiring different approaches for data fitting. The choice of approach and computer program is usually subjective, and it is generally assumed that this choice has no influence on the obtained parameter estimates. However, this assumption has not yet been verified comprehensively. Therefore, in this study, five computer programs for progress curve analysis were compared with respect to accuracy and minimum data amount required to obtain accurate parameter estimates. While two of these five computer programs (MS‐Excel, Origin) use algebraic parameter estimation, three computer programs (Encora, ModelMaker, gPROMS) are able to perform dynamic parameter estimation. For this comparison, the industrially important enzyme penicillin amidase (EC 3.5.1.11) was studied, and both experimental and in silico data were used. It was shown that significant differences in the estimated parameter values arise by using different computer programs, especially if the number of data points is low. Therefore, deviations between parameter values reported in the literature could simply be caused by the use of different computer programs.     

Sequence data handling by computer.

The speed of the new DNA sequencing techniques has created a need for computer programs to handle the data produced. This paper describes simple programs designed specifically for use by people with little or no computer experience. The programs are for use on small computers and provide facilities for storage, editing and analysis of both DNA and amino acid sequences. A magnetic tape containing these programs is available on request.     

Some practical aspects of computer applications in a fermentor hall

The use of computers in a fermentation pilot plant is described from a practical point of view. The aim is not the application of a computer to a single special process but a general application of computers to prepare and present data for the following analysis of fermentation processes. The hardware is normally bought from computer manufacturers, but some additional installations are useful. Application software has to be developed by the biotechnologist, therefore the software structure is the most important part of the computer application. Data storage is divided into three parts: short-time memory, long-time storage, and a medium memory mainly to be used in process analyses and process control. Four types of programs are used: main schedule tasks, low-priority on-line tasks, sense-switch routine, and different off-line programs. A table of all programs is presented, the main schedule task is described in detail to demonstrate the software structure.     

中国种子植物区系定量化研究 Ⅱ.多地区种子植物区系研究实用程序工作原理(DDBJ-系列程序)

本文介绍了定量化研究多个种子植物区系的电子计算机程序（DDAI）工作原理,简要讨论以共有属构建的区系间相似关系问题。应用本文提出的程序,可一次性完成所有被研究区系种子植物分布区类型的统计及有关的计算工作,同时也可根据各分布区类型及总体共有属,构建各个区系间的相似性系数及其他有关的参数。本文以中国若干种子植物区系原始资料统计计算为例提供的CAR（Computer Aided Research）方法,可对全面深入地研究中国种子植物区系,提供强有力的工具。     

Microcomputer programs for DNA sequence analysis.

Computer programs are described which allow (a) analysis of DNA sequences to be performed on a laboratory microcomputer or (b) transfer of DNA sequences between a laboratory microcomputer and another computer system, such as a DNA library. The sequence analysis programs are interactive, do not require prior experience with computers and in many other respects resemble programs which have been written for larger computer systems (1-7). The user enters sequence data into a text file, accesses this file with the programs, and is then able to (a) search for restriction enzyme sites or other specified sequences, (b) translate in one or more reading frames in one or both directions in order to find open reading frames, or (c) determine codon usage in the sequence in one or more given reading frames. The results are given in table format and a restriction map is generated. The modem program permits collection of large amounts of data from a sequence library into a permanent file on the microcomputer disc system, or transfer of laboratory data in the reverse direction to a remote computer system.     

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.     

Representation of a protein molecule as a tree and application to modular computer programs which calculate and modify atomic coordinates

The concept and representation of a logical tree as defined in computer science is applied to obtain a suitable representation of protein molecules in computer programs which handle or calculate atomic coordinates of protein molecules. On the basis of this analysis and of the analysis of the calculation and modification of the structure of a protein from bond lengths, bond angles, and dihedral angles, which is reproduced in an appendix, program modules which accomplish the various required computations are described. Three such modules are given in Iverson notation; in fact, it is hoped that this article will serve as a reasonably complete basis for the preparation of machine programs by moderately proficient programmers.     

Portable microcomputer software for nucleotide sequence analysis.

The most common types of nucleotide sequence data analyses and handling can be done more conveniently and inexpensively on microcomputers than on large time-sharing systems. We present a package of computer programs for the analysis of DNA and RNA sequence data which overcomes many of the limitations imposed by microcomputers, while offering most of the features of programs commonly available on large computers, including sequence numbering and translation, restriction site and homology searches with dot-matrix plots, nucleotide distribution analysis, and graphic display of data. Most of the programs were written in Standard Pascal (on an Apple II computer) to facilitate portability to other micro-, mini-, and and mainframe computers.     

花粉形态计算机量化分析研究

以白莲花粉为实验材料 ,介绍了进行花粉形态计算机量化分析的步骤。花粉经醋酸法处理后 ,用电子显微镜对花粉进行观察照相 ,尔后用计算机技术对花粉电镜照片进行处理 ,最后用C语言编制了计算花粉形态面积的计算机程序。结果表明 :花粉计算机量化分析有助于快速定量测定有关花粉形态指标 ,是花粉数量分类的一种有效方法。     

GENEUS, a computer system for DNA and protein sequence analysis containing an information retrieval system for the EMBL data library.

We describe a comprehensive computer system, GENEUS, for extensive DNA, RNA and protein sequence analysis. The analysis system is developed for the DEC VAX/VMS computer and uses the EMBL Nucleic Acid Sequence Data Library. Help information is available on-line on terminal screen. To speed up system handling, a qualifier oriented user communication is employed. All results are stored on files making them accessible to the computer editor. An information retrieval system for the EMBL Nucleotide Sequence Data Library is also described. A defined data-base interface allows connection to other analysis programs.+     

花粉形态计算机量化分析研究

以白莲花粉为实验材料,介绍了进行花粉形态计算机量化分析的步骤。花粉经醋酸法处理后,用电子显微镜对花粉进行观察照相,尔后用计算机技术对花粉电镜照片进行处理,最后用C语言编制了计算花粉形态面积的计算机程序。结果表明：花粉计算机量化分析有助于快速定量测定有关花粉形态指标,是花粉数量分类的一种有效方法。     

A low-cost system for computerized rodent weight logging with statistical analysis

A system comprising a suite of 4 computer programs has been developed for on-line rodent weight data collection and statistical analysis using an IBM personal computer. Data can be collected from up to 3 separate trials simultaneously, and can be stored for later statistical analysis. Mettler balances were used for the animal weighing. A Mettler current loop adapter and a multiplexer were used to interface the balances with the computer.     

Automated analysis of NMR assignments and structures for proteins.

Recent developments in protein NMR technology have provided spectral data that are highly amenable to analysis by advanced computer software systems. Specific data collection strategies, coupled with these computer programs, allow automated analysis of extensive backbone and sidechain resonance assignments and three-dimensional structures for proteins of 50 to 200 amino acids.     

Further procedures for sequence analysis by computer

A previous paper¹ described programs for sequence data handling and analysis by computer. The facilities of this basic set are extended by further easily used programs.     

A strategy of DNA sequencing employing computer programs.

With modern fast sequencing techniques and suitable computer programs it is now possible to sequence whole genomes without the need of restriction maps. This paper describes computer programs that can be used to order both sequence gel readings and clones. A method of coding for uncertainties in gel readings is described. These programs are available on request.     

A collection of programs for nucleic acid and protein analysis, written in FORTRAN 77 for IBM-PC compatible microcomputers.

We have developed a collection of programs for manipulation and analysis of nucleotide and protein sequences. The package was written in Fortran 77 on a Sirius1/Victor microcomputer which can be easily implemented on a large variety of other computers. Some of the programs have already been adapted for use on a Vax 11. Our aim was to develop programs consisting of small, comprehensible and well documented units that have very fast execution times and are comfortably interactive. The package is therefore suitable for individual modifications, even with little understanding of computer languages.     

Evaluation of the normal equations for the analysis of diallels

Summary Analysis of diallel experiments usually requires specialised computer programs. A simple relationship between the normal equations for a diallel and the normal equations for a hypothetical model in which the general combining ability factor is viewed as two separate distinct simple factors may be useful in adapting general statistical analysis packages to the desired analysis.     

A microcomputer system for the measurement of finger forces

In the analysis of hand functions, the production and control of forces exerted during voluntary contraction of the finger muscles plays an important role; unfortunately such an analysis is rarely seen in routine clinical examinations of neurological patients. A microcomputer controlled system for the measurement and analysis of finger forces is described. The system consists of a modified Z80 based microcomputer, a commercially available high precision force transducer, a specially designed force signal amplifier and a suite of menu-driven user interactive programs. A variety of tasks is implemented by means of the computer programs. In addition to the measurement of maximum hand grip force, the system is able to record forces continuously as a function of time. Task characteristics and the type of feedback presented to the subject are under user control; they can be varied to meet clinical or experimental requirements. Examples of programs and clinical applications are presented and discussed.     

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.