Web-based publications

The accuracy of the references is the author s responsibility. Errors in references are one of the most common errors found in scientific publications and are a source of frustration to readers. Increasingly, hypertext links are automatically generated in Web-based publications, but this cannot be done for references containing errors. If citations are copied from another source, check the original reference for accuracy and appropriate content. 

References are an important component of every scholarly manuscript. Having complete and accurate references is the author s responsibility. Errors in references are one of the most common mistakes authors make. Although correct citations have always been important, the increasing number of hypertext links in Web-based publications makes correct citations more important than ever. Given the volume of manuscripts that publishers produce yearly, technical editors cannot verify each reference in each manuscript. 

Reminder Although correct citations have always been important, the increasing number of hypertext links in Web-based publications makes correct citations more important than ever. 

As draft species accoimts were collated and compiled, the material was adjusted to fit standardised presentation formats. This should ultimately be available as both online pages and PDF files, ready for web-based publication and easily translated into hard copy. 

The JME Editor is a Java program which allows one to draw, edit, and display molecules and reactions directly within a web page and may also be used as an application in a stand-alone mode. The editor was originally developed for use in an in-house web-based chemoinformatics system but because of many requests it was released to the public. The JME currently is probably the most popular molecule entry system written in Java. Internet sites that use the JME applet include several structure databases, property prediction services, various chemoinformatics tools (such as for generation of 3D structures or molecular orbital visualization), and interactive sites focused on chemistry education [209]. 

It is worth noting that the past few years have witnessed tremendous development of web-based information resources. Notably, the PubMed search tool [4] has made the investigation of any life sciences topic much easier. It offers keyword and author (as well as structure and sequence) searches and covers a wide range of medicinal chemistry-related journals. This resource, coupled with e-journals, affords the medicinal chemist the tools to keep up with any research topics of interest. Because of the public nature of the Web, now a chemist can sometimes find critical journal articles on the Web that do not show up until much later in traditional literature sources. It is not uncommon that scientific meeting presentations can be found on the Web. Indeed, the Internet tools we have all become familiar with also have made the professional life of the medicinal chemist much easier. 

A survey of computer use in university courses has been carried out by Miles and Francis 149). Due to poor response rate of a Web-based questionnaire, the findings were skewed toward those faculty members who were using computers in their course. The most widely used application among the respondents was the spreadsheet, while the use of molecular modeling, and symbolic mathematics software lagged behind. The authors recommended that teachers should develop more computer-based activities, exploit fully the Web resources, and transfer effectively technical skills. They also provided a list of relevant Web sites, but in the time elapsed since that publication, the currently available Web material must be greatly enhanced, both in terms of number of materials available and in terms of quality of content. 

Because formatting within an electronic resume is often minimal, what you say within your resume is what ultimately gets you hired. According to www.eresumes.com, "Keywords are the basis of the electronic search and retrieval process. They provide the context from which to search for a resume in a database, whether the database is a proprietary one that serves a specific purpose, or whether it is a web-based search engine that serves the general public. Keywords are a tool to browse quickly without having to access the complete text. Keywords are used to identify and retrieve resumes for the user. 

This increased information is likely to come from a number of sources. The popularity of web-based medical advice sites (independent, disease association sponsored, and drug manufacturer sponsored) has already been established. These sites serve both the general public directly and the medical establishment which in turn informs (often with clarification and interpretation) the public. Use of such sites is likely to increase as patients and their providers seek more and better sources of detailed information. 

A second initiative is being developed by Dr. Ann Richard and coworkers at the EPA. The Distributed Structure-Searchable Toxicity (DSSTox) public database network is a flexible community-supported, web-based approach for the collation of data. It is based on the SDF format for the representation of chemical structure. It is intended to enable decentralized, free public access to toxicity data files. This should allow users from different disciplines to be linked. Public, commercial, industry, and academic groups have also been asked to contribute to, and expand, the DSSTox public database network. Data from potentially any toxicological endpoint can be collated in the DSSTox public database network, including both human health, and environmental endpoints (Richard et al 2002 Richard and Williams, 2002). 

The IUCr Web site (http //www.iucr.org/iucr-top/cif/) lists other software that can be used to manipulate or visualize CIF content. Most importantly, they maintain a Web-based service that provides a classihed validation report on any format-compliant CIF. This service can be accessed at http //checkcif.iucr.org/. CheckCIF reports can be lengthy, but it is wise to scan them carefully, particularly the most serious Class A alerts. Journal editors and their referees will often indicate the types of alerts that they would normally expect to be fixed by the authors before publication. 

Whereas chemical structures will always be the primary vehicle for visual communication, it is possible that journal articles will be reporting a unique label representing a chemical structure in the near future, especially because this label will already allow the searching of chemical structures contained in publications indexed using Web-based search engines. For more on this, see Appendix 8-1. 

In this chapter, we extend the one-dimensional MRTM transport and adsorption model (Zeng et al., 2002 Selim et al., 1990) to three-dimensional applications, using the altemating-direction-implicit (ADI) numerical algorithm to reduce computational complexity. We also discuss the development of a web-based system with a user-friendly interface providing client-side and server-side computing applications and web-based visualization functionality. The accuracy and efficiency issues of solution algorithms will be addressed in future publications. 

Web-based applications used in GxP-critical processes are no different than other GxP appli-eations and should be validated and subject to appropriate operation compliance procedures. However, Web-based applications are in principle readily accessible by the general public and therefore must be subject to secure rrser access controls. Eurther, having gained access to the particular application, it must not be possible to gain access to other applications located on the infrastructure. 

Augmenting the CD version of CASSl is the CAS Source Index (CASSl) Search Tool (http //cassi. cas.org/search.jsp). Available from January 2010, the CASSl search tool is a free, web-based resource that can be used to quickly identify or confirm journal titles and abbreviations for publications indexed by CAS since 1907, including serial and non-serial scientific and technical publications. 

These three special issues of the journal Toxicology provide a comprehensive overview of Web-based toxicology resources that are available to the public. Part I focuses on government resources, including those of the US EPA and various other federal agencies, subnational toxicology information resources (state, territorial, tribal, municipal, and community),... 

SuperScent is a database comprising approximately 2000 scents (Dunkel et al., 2008). The database can be browsed online and includes web-based similarity searching. The molecules are linked to PubChem (vide infra). Additional databases in the "Super" collection are Super-Toxic, SuperSite, and SuperTarget. The SuperScent web site (Table 2.2) has links to other public databases such as SenseLab, Pherobase, Scentbase, Flavomet, and Leffingwell. 

The MMsINC database (Masciocchi et al., 2009) is a public web-based resource with more than 4 million nonredundant compounds for virtual screening and other computational applications. Substructure and similarity searching can be performed. MMsINC is linked to other databases such as FDA, PubChem, Protein Data Bank, and ZINC. 

Table 2.2 also lists three publicly available databases commonly used in drug research. PubChem is accessed through the National Library of Medicine (Austin et al., 2004) and contains chemical structure information and corresponding activity across a number of biological assays. The system links the compound information with biomedical literature and it is possible to perform web-based similarity searching. PubChem also enables one to download files with structures to perform chemoinformatic analysis off-line. 

As indicated, most MS manufacturers have designed their own metabolomic software, which is often provided with the MS operating software. These programs are usually not as flexible as the open-source software as they do not permit modifications to operating algorithms and parameter optimization can also be limited. Commercial software can also perform multivariate statistical analysis such as principal component analysis. Recent versions can also be directly linked to public databases for Web-based searches toward marker identification. 

Pathway Commons (http //www.pathwaycommons.org) is a freely available database that collects, normalizes, and integrates publicly available biological pathway and molecular interaction data about cellular processes. It is a collection of publicly available pathway data from multiple organisms. Pathway Commons provides a Web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources (16). Users can ask questions such as What proteins interact with a protein under study , What pathways involve a given protein , Is a specific protein involved in transport events or biochemical reactions , or What enzymes use a specific metabolite as a substrate . 

Since February, 2002, Dr. Friedewald has been Medical Director of Argusl, a Web-based program for the early detection of biological and chemical attack and other naturally-occurring and accidental public health threats. Argusl is used for point-of-care decision support by physicians, physicians assistants, muses, first responders... 

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