Directory Structure

The subdirectories GLUCOSE and OLIGOSAC have both the same substructures  

The file names, e.g. GHHCODF, of the NMR data sets as shown in Fig. 2.7 and stored in the subdirectories C, H, IDREF, CH and HH include information on the sample, the type of spectrum (1D/2D) and the experiment itself. The meanings of the various ubbreviation.s are listed below  

CHI 2D H/ C shift correlation spectrum with H detection ( inverse  

In chapter 3 the basic theory and the application of these experiments to obtain structural information is briefly discussed and examples of corresponding spectra obtained for the peracetylated p-D-glucose are depicted. 

---

FIGURE 4 A typical directory structure found in a flat-file data system. 

A published synthetic scheme (36) of a four component Ugi reaction (Fig. 6) has been used as an example to demonstrate the use of the SA optimization protocol for the simultaneous optimization of multiple properties. Because two of the four components are fixed in the scheme, only two diversity sites remain for optimization. These two sites come from primary amines (R1NH2) and aldehydes (R2CHO), respectively. We have collected from the ACD (Available Chemical Directory) structures of primary amines and aldehydes available from ALDRICH and LANCASTER. Compounds with reactive or unstable structural patterns are removed. As a result, 779 primary amines and 246 aldehydes are considered. 

Fig. 2.9 shows the main directory structure and the structure of two subdirectories of the NMR data base stored on your CD-ROM as displayed by the WINDOWS File manager. If it is planned to copy the NMR data from your CD-ROM onto your hard disk to speed up further processing, the same directory structure should be established there (see 2.5.5). Note, however, that ID WIN-NMR generates additional auxiliary subdirectories (AU, DAT, NMR, PC, TMP) in the directory DEMOID on your harddisk. 

Fig. 2.9 Main directory structure of the NMR data base NMRDATA (left), of the GLUCOSEMD (middle) and of the GLUCOSBCD subdirectory (right).

Start the WINDOWS Explorer and check there is 150-200 MBytes of space available on one of your hard disk(s). Follow one of the standard procedures for copying files from one to another directory. Consult the WINDOWS manual, or first study the Check it instructions for copying a file or directory given in the next section (2.5.6), if necessary. Select in your CD-ROM the directory NMRDATA or any of its subdirectories and copy it to disk D on your PC. The directory NMRDATA GLUCOSE 1D H and a few auxiliary directories therein (see 2.5.4) have already been created during installation of ID WIN-NMR. Answer the corresponding question for overwriting all files stored under the same name with yes. Use the WINDOWS Explorer) to inspect the newly created NMR data directory NMRDATA on your hard disk. Click on several items in this directory and familiarise yourself with the directory structure. 

By default Matlab will be installed in the directory C matlabrxx on your PC, where xx relates to the edition of the package. You can choose to install elsewhere but at first it is best to stick to the standard directories, which we will assume below. You need some knowledge of DOS directory structure to use the directory commands within Matlab. According to particular combinations of versions of Windows and Matlab there is some flexibility, but keeping to the commands below is safe for the first time user. 

For smaller systems, such as personal computers, the data and programs may be located on the same disk and partitioned by the directory structure. If the backup software is capable of performing selective backups, the comments in the paragraph above apply. However, if there is little sophistication, the whole disk may have to be backed up routinely. Again, for PC systems this may be an area to evaluate closely before buying. An alternative is a PC network where the programs and data are held on a central server and can be backed up more efficiently and effectively than stand-alone systems. 

Directory structure Software construction File header and commenting Version control File naming conventions... 

Folder/directory structures File structures File sizes File properties File access Storage media Storage capacity Data retrieval rates User interfaces... 

Correct folder/directory structure created and files installed within folders/directories Software configuration completed satisfactorily Site and system identification User access groups Security configuration Menu/display access configuration Logical device connections Inspection of critical hardware components Servers in correct locations Processor speed Cache size ROM bios Memory capacity Peripherals Storage devices Input devices... 

Electronic records should be saved in a well-designed directory structure that is strictly controlled. This includes measures such as backup and access restrictions. An example organization of data is shown in Figure 32.5. General security and administration are discussed in Chapter 12 of this book. 

Every project should indicate the mandatory documented program coding standards, directory structure standards, file naming conventions, and configuration management processes that are expected to be undertaken for all coding output. AU of these documents should be readily available, either in electronic or hard copy, for all staff to consult as necessary. 

In the formal specification of version 2.0, ontology modules are manifested through different XML namespaces [1060], each of which is stored in a single OWL file connections between the modules are realized by using the import mechanism provided by OWL. The partial models correspond to identically named directories in the formal specification. That way, they establish a directory structure for managing the OWL files. 

Standardized directory structures for source code, documentation hies, hnal executables, conhguration hies, and model inputs/outputs allow tracking the software development process and also help in easily integrating multiple, independently developed modules. Standardized directory structures allow easy detection of con-hicts in the names of functions, scripts, or conhguration hies. 

Align all sequence files in directory structure (13 hours)... 

The full version of the NMR-SIM program can be purchased either as the Windows NTAVindows 2000 version or the UNIX version from BRUKER. These versions use the same program set-up and commands as the Teaching version or though by necessity the directory structure of the UNIX version is different. For further details the reader is invited to contact BRUKER or their local representative directly, the contact addresses are listed on BRUKER s worldwide web homepage [1.13, 1.14]. 

Fig. 1.2 shows the directory structure generated by the software installation using the recommended directory. The main TEACH directory contains the program subdirectories Getfile, NMR-Sim, Win ID and Win2D plus the data subdirectory Nmrdata. The subdirectories Manuals and Results contain the software documentation for the programs and the additional information and results for most of the Check its. 

Fig. 1.2 Directory structure - Software, data and documentation subdirectories installed according Check its 1.2.11 and 1.2.1.3.

After the software installation two new directories will have been created in the root directory of the local PC. Assuming that the default pathway was used in the installation the program directory C Teach. .. has the directory structure shown in Fig. 1.2. The second directory C NMRSIM SESSION created contains all the pulse programs, spin systems and experimental set-ups files in the subdirectories C . .. CONFIG configuration files, C . .. HAM spin system files, C . .. PP pulse program files, C . .. WAVE pulse shape files, C . .. LIST lists files and C . .. JOB job files. Table... 

Fig. 1 Illustration of the basic directory structure within Wolf2Pack. Each molecule with a given conformation has its own parent directory. The number of bond, angle, and torsion subdirectories is dependent upon the molecule s unique internal coordinates. The QM n and EF n labels indicate data from constraint QM and MM optimizations using a specific theory level (e.g., HF/6-31G(d)//HF/6-31G(d)) or force field (e.g., Parml4SB)...

Thus, the logical file system uses a file directory structure of some form to link the reference to a symbolic file name of the user s choosing with the location (and perhaps type) of the file. It is at this level of the system that the file directory structure and format are determined and where directory entries are made, changed, and deleted. There are four basic forms of directory (a given operating system will use only one). 

Disk access is commonly the performance bottleneck in systems. To avoid any more disk access than strictly necessary, the operating system will keep a table of open files in memory, with the file identifier (which may not be the symbolic name) and a pointer to the next disk block to be read or written (the current-flle-position pointer). The table is updated whenever a file is opened, and again when it is closed (at which time the entry is copied back to the disk s directory structure). 

The final directory structure of the tutorial should be similar to this figure. 

The project manual is often associated with a certain order systematics. This means either a directory structure for computer files or a systematics for the description of files. In both cases the fiUng of and access to documents shall be made easier for the employees involved. Tables 4.5 and 4.6... 

While CandidTree was originally developed to show structural uncertainty, it can also be applied to visualize the differences between two tree structures. For example, when we have two (backup) directory structures (for two different time points) containing backups for the same folder, CandidTree can help users find added, deleted, or moved files, in addition to modified folders. Furthermore, it enables users to identify which folder has been changed the most or least. 

To identify major usability issues, we conducted a preliminary usability study with six participants two researchers, three developers, one research intern (all male computer scientists). We used two sets of backup directory structures, each with two trees representing the data at two different time points. Trees in these sets contained about 150... 

We proposed two types of uncertainty for tree structures - location and sub-tree structure uncertainty - based on the differences between them. To visualize those structural uncertainties, a new interactive visualization system called CandidTree was developed. Since CandidTree computes uncertainty by comparing two trees, we were able to apply it to visualize the differences between them. For example, CandidTree helps users find added, deleted, or moved files as well as modified folders within two (backup) directory structures containing backups for the same folder. 

Future improvements will consider the improvement of interaction techniques, the use of linked views for the visualization of the directory structure of baselines and the comparison of several baseline structures. Furthermore, a usability test to compare the three dimensional representation and Revision Tree will be conducted. 

One flaw of this scheme is that identical documents served from multiple sites have different URLs. Also, URLs leading to the same document can become different if the server host has more than one name, or file system links are modifying the directory structure of the server. An alternative to the URL scheme called URN (uniform resource names ) is currently being discussed. A URN is an unique identifier of a document similar to an ISBN number, making copies and different versions of documents identifiable. The latest proposal in this area, backed by many scientific publishers, is the DOI (digital object identifier). 

---