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The use of microsoft excel as a user interface for biological simulations
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Monitor ARTHUR C ROBINSON Department of Biological Sciences Napier University Edinburgh EHIO 5DT, UK Sfinchez-Ferrer A, Niifiez-Delicado E and Bru R Software for Viewing Biomolecules in Three Dimensions on the Internet. TIBS 20, (July) 286-288 1995. Faced with the problem of developing, without financial support, a practical course on protein and nucleic acid structure, the authors searched the Internet for free distribution and shareware programs. After extensive searching they report here on several public domain programs and a commercial package that partially solved their problem. All of the programs are accessible by anonymous file-transfer protocol (ftp). The programs are: RasMol 2.5 {ftp.dcs.ed.ac.uk (129.215.160.5)}; pdVwin {nemo.life.uiuc.edu (128.174.183.6)} Prekin 2 4 and Mage_2__4 {ftp.uci.edu (128.200.15.20)}; HyperChem 3.0 (Demo) {ftp.bio.indiana.edu (129.79.224.25)}. The authors summarise their experiences with these programs. RasMol 2.5 runs on a wide variety of platforms from workstations to personal computers, but behaves identically on all, with only the loading and start-up being different, depending on the operating system. Two windows are displayed: a graphics window and a command-line window, and the program can handle a variety of molecular co-ordinate file formats, including those from the Brookhaven Protection Databank (PDB). The selected molecule can be displayed in different forms (sticks, backbone, space-filling spheres etc), colours changed, the molecule rotated and zoomed interactively using the mouse or the scroll bars. RasMol is distinguished from the other programs by allowing interactive commands to be typed in the commandline window. This permits the selection and labelling of specific zones of a molecule. pdVwin (also called pdViewer and available only for Windows 3.1) has the useful feature of allowing the simultaneous loading of two protein database files in two model storage areas; a feature that allows two structures to be superimposed on one another. A "Rock It" option flips the model back and forth between two stereo pair views, giving the impression of a threedimensional image. The output of a file containing d~ and angles of the polypeptide chain can be viewed as a Ramachandran plot using the included ramachan.exe program. Prekin and Mage allow the production and viewing respectively of three-dimensional images of macromolecules. Their particular attraction from the teaching point of view is that they allow switching between two or more conformations. This is especially useful when demonstrating the subtle conformational changes which occur during the interaction between an enzyme and its substrate, for example. HyperChem converts a two-dimensional sketch of a molecule into a three-dimensional model, it generates a macromolecule (polypeptide or nucleic acid) from selected amino acid residue or nucleic acid dialogue boxes, and allows the measurement of bond distances, bond angles and torsion angles, and can simulate the movement of molecules in their solvent. The authors recommend the use of a combination of these programs for teaching purposes, since each program has its own particular strengths and weaknesses. HyperChem was judged to be the only program suitable for the generation of simple structures. It permits a novice to build and mutate a polypeptide secondary structure or a polynucleotide sequence by clicking on the desired residue as described above. Students also produced attractive results when "building" sugars and lipids. It is suggested that, once a molecule has been constructed with HyperChem, it is best exported in PDB format for use in other
BIOCHEMICAL
EDUCATION
23(4) 1995
programs. RasMol is recommended for the study of motifs, domains and the tertiary structures of proteins and nucleic acids (tRNA). This is because it is easy to select, label, rotate and highlight different parts of the molecule using the command line window. RasMol is again recommended as being the more flexible and didactic program for illustrating protein-protein and protein-nucleic acid interactions, although Mage is also useful here. Not all the features of the above programs can be described in this review, and the interested reader is referred to the original publication for more detailed information. [Departamento de Bioquimica y Biologfa Molecular (A), Facultad de Biologia, Universidad de Murcia, E-30001 Murcia, Spain]
Tack G, Roselli R J, Overholser K A and Harris T R The Use of Microsoft Excel as a User Interface for Biological Simulations. Computers and Biomedical Research 28, 24-37 (1995) Most biological simulation programs manipulate input and output data files and must be run extensively in order to test different initial conditions, and to see the effects of changing several different parameters. Changing input parameter values and monitoring the effects of these changes is a very tedious process using ASCII input and output files, but this tediousness can be avoided by using a user-friendly interface such as that found in many commercial Windows-based programs. Although it is difficult to design a stand-alone user interface, it is relatively easy to use the built-in features of commercial programs to manipulate input and output information. The authors have used Microsoft Excel 4.0 for Windows running on a PC-486 to develop a user interface for two biological simulations: a lung fluid balance model and a fractal model of pulmonary circulation. They chose Excel for Windows because it has a built-in macro language together with a wide range of graphics utilities which are ideal for handling biological simulation problems. Other advantages of using Excel include: the ease of changing the size and form of graphs, the familiarity of the Excel interface, the ability to include calculations, the provision of context-sensitive help routines, and the provision of built-in error messages. The simulation programs were written in the C programming language, and compiled using Borland C+ + 4.0, while the user interface was written using the Excel macro language. The interface builds input data files for the simulation programs and displays relevant information from output files produced from the simulations. Partial protection of input fields ensures that the user cannot modify certain crucial parts of the spreadsheet. The Excel interface is used to build models from different available components and to select appropriate parameters for the models. Models can also be run in batch mode, a facility which permits several different models to be run at once in the background: a useful provision when several long simulations are to be run, or when a sensitivity analysis for one or more parameters is required. The authors report some minor problems with exceeding the memory capacity of their PC (8 MB), but note that their initial programming with the latest version of Excel (version 5.0) using the new Visual Basic interface released more memory for data manipulation compared to version 4.0. They conclude by stating that the techniques used in developing their user interface can be extended to most biological simulation programs which manipulate input and output data files. [Department of Biomedical Engineering, Vanderbilt University, School of Engineering, Nashville, Tennessee, USA]
Monitor ARTHUR C ROBINSON Department of Biological Sciences Napier University Edinburgh EHIO 5DT, UK Sfinchez-Ferrer A, Niifiez-Delicado E and Bru R Software for Viewing Biomolecules in Three Dimensions on the Internet. TIBS 20, (July) 286-288 1995. Faced with the problem of developing, without financial support, a practical course on protein and nucleic acid structure, the authors searched the Internet for free distribution and shareware programs. After extensive searching they report here on several public domain programs and a commercial package that partially solved their problem. All of the programs are accessible by anonymous file-transfer protocol (ftp). The programs are: RasMol 2.5 {ftp.dcs.ed.ac.uk (129.215.160.5)}; pdVwin {nemo.life.uiuc.edu (128.174.183.6)} Prekin 2 4 and Mage_2__4 {ftp.uci.edu (128.200.15.20)}; HyperChem 3.0 (Demo) {ftp.bio.indiana.edu (129.79.224.25)}. The authors summarise their experiences with these programs. RasMol 2.5 runs on a wide variety of platforms from workstations to personal computers, but behaves identically on all, with only the loading and start-up being different, depending on the operating system. Two windows are displayed: a graphics window and a command-line window, and the program can handle a variety of molecular co-ordinate file formats, including those from the Brookhaven Protection Databank (PDB). The selected molecule can be displayed in different forms (sticks, backbone, space-filling spheres etc), colours changed, the molecule rotated and zoomed interactively using the mouse or the scroll bars. RasMol is distinguished from the other programs by allowing interactive commands to be typed in the commandline window. This permits the selection and labelling of specific zones of a molecule. pdVwin (also called pdViewer and available only for Windows 3.1) has the useful feature of allowing the simultaneous loading of two protein database files in two model storage areas; a feature that allows two structures to be superimposed on one another. A "Rock It" option flips the model back and forth between two stereo pair views, giving the impression of a threedimensional image. The output of a file containing d~ and angles of the polypeptide chain can be viewed as a Ramachandran plot using the included ramachan.exe program. Prekin and Mage allow the production and viewing respectively of three-dimensional images of macromolecules. Their particular attraction from the teaching point of view is that they allow switching between two or more conformations. This is especially useful when demonstrating the subtle conformational changes which occur during the interaction between an enzyme and its substrate, for example. HyperChem converts a two-dimensional sketch of a molecule into a three-dimensional model, it generates a macromolecule (polypeptide or nucleic acid) from selected amino acid residue or nucleic acid dialogue boxes, and allows the measurement of bond distances, bond angles and torsion angles, and can simulate the movement of molecules in their solvent. The authors recommend the use of a combination of these programs for teaching purposes, since each program has its own particular strengths and weaknesses. HyperChem was judged to be the only program suitable for the generation of simple structures. It permits a novice to build and mutate a polypeptide secondary structure or a polynucleotide sequence by clicking on the desired residue as described above. Students also produced attractive results when "building" sugars and lipids. It is suggested that, once a molecule has been constructed with HyperChem, it is best exported in PDB format for use in other
BIOCHEMICAL
EDUCATION
23(4) 1995
programs. RasMol is recommended for the study of motifs, domains and the tertiary structures of proteins and nucleic acids (tRNA). This is because it is easy to select, label, rotate and highlight different parts of the molecule using the command line window. RasMol is again recommended as being the more flexible and didactic program for illustrating protein-protein and protein-nucleic acid interactions, although Mage is also useful here. Not all the features of the above programs can be described in this review, and the interested reader is referred to the original publication for more detailed information. [Departamento de Bioquimica y Biologfa Molecular (A), Facultad de Biologia, Universidad de Murcia, E-30001 Murcia, Spain]
Tack G, Roselli R J, Overholser K A and Harris T R The Use of Microsoft Excel as a User Interface for Biological Simulations. Computers and Biomedical Research 28, 24-37 (1995) Most biological simulation programs manipulate input and output data files and must be run extensively in order to test different initial conditions, and to see the effects of changing several different parameters. Changing input parameter values and monitoring the effects of these changes is a very tedious process using ASCII input and output files, but this tediousness can be avoided by using a user-friendly interface such as that found in many commercial Windows-based programs. Although it is difficult to design a stand-alone user interface, it is relatively easy to use the built-in features of commercial programs to manipulate input and output information. The authors have used Microsoft Excel 4.0 for Windows running on a PC-486 to develop a user interface for two biological simulations: a lung fluid balance model and a fractal model of pulmonary circulation. They chose Excel for Windows because it has a built-in macro language together with a wide range of graphics utilities which are ideal for handling biological simulation problems. Other advantages of using Excel include: the ease of changing the size and form of graphs, the familiarity of the Excel interface, the ability to include calculations, the provision of context-sensitive help routines, and the provision of built-in error messages. The simulation programs were written in the C programming language, and compiled using Borland C+ + 4.0, while the user interface was written using the Excel macro language. The interface builds input data files for the simulation programs and displays relevant information from output files produced from the simulations. Partial protection of input fields ensures that the user cannot modify certain crucial parts of the spreadsheet. The Excel interface is used to build models from different available components and to select appropriate parameters for the models. Models can also be run in batch mode, a facility which permits several different models to be run at once in the background: a useful provision when several long simulations are to be run, or when a sensitivity analysis for one or more parameters is required. The authors report some minor problems with exceeding the memory capacity of their PC (8 MB), but note that their initial programming with the latest version of Excel (version 5.0) using the new Visual Basic interface released more memory for data manipulation compared to version 4.0. They conclude by stating that the techniques used in developing their user interface can be extended to most biological simulation programs which manipulate input and output data files. [Department of Biomedical Engineering, Vanderbilt University, School of Engineering, Nashville, Tennessee, USA]