Genome Biology | information

About the Genome Biology website

This page provides a short guide to the Genome Biology website structure, an explanation of the symbols used and an idea of new article types and functionalities you can expect to see over the coming months.

If you can't find the information you need, or if you have any comments about the site, please e-mail us.

You should find the Genome Biology website quick and easy to use, and its structure is designed to provide a robust framework for us to expand and develop the site in the future.

The structure of the Genome Biology website

Overview

Some key information appears at the tope of every page within the Genome Biology website. At the very top is a gray bar that welcomes you (by name if you have registered), indicates when you last visited, and provides quick navigation to the Genome Biology website homepage, support pages (which include customer support, frequently asked questions and this web guide), feedback forms and a button to allow users to log on or off. At the extreme right is today's date (in London).

Moving down each page, after a white space that includes our logo and can include advertisments, you will see a black navigation bar. From this, you can browse the major sections that make up both the website and the printed Genome Biology journal.

The homepage for each major section of the journal (that is, each section included on the black navigation bar) can be accessed by typing the section name after Genome Biology (for example http://genomebiology.com/reviews). Individual articles have a unique URL that denotes the year of publication, volume and issue numbers, and it's article number - for example http://genomebiology.com/2005/6/12/242. This URL can be translated into a traditional citation format as follows: Genome Biology 2005, 6(12):242

Once within a section of the website, subheadings appear on the right of the page below the black navigation bar. You can use these to explore further within that section; each one indicates a subsection that includes a single type of article within that section of the journal (for example, minireviews) and options for viewing articles (for example, sort by date). You can return to the main page for that section (or any other section) any time by clicking on the relevant section name in the black menu bar.

On the left of each section home page, a gray column provides information about the section. Some of this information is reproduced below.

Major sections of the journal

| home |

The Genome Biology homepage lists the editor's selection of the most interesting new content from all sections of the journal. Content from other resources from the same publisher, BioMed Central, that might be of interest to readers, are highlighted in the left-hand gray bar.

| comment |

Access to all comment, opinion and editorial articles, and to the full archive of research news, which was previously published regularly in association with The Scientist. Genome Biology publishes opinion pieces, commentaries and editorials on a broad range of topics, including political, scientific, and medical issues relating to genomic, post-genomic and genome-scale analyses. Readers are encouraged to participate in discussions and to comment on articles via the website.

| reviews |

Access to the reviews homepage. From here listings of all reviews, minireviews, protein family reviews and tutorials can be accessed. Genome Biology aims to provide review material that readers need in order to assess and evaluate progress in genomic and post-genomic research. Reviews include systematic and substantial coverage of mature subjects, rapid coverage of fast-moving areas, evaluations of progress in specified areas, and critical assessments of emerging technologies, as well as structured reviews of individual protein families and tutorial 'beginners' guides' to tools and resources.

| reports |

Genome Biology regularly publishes meeting reports which are short and rapidly prepared and report on information presented at conferences. Paper and web reports highlight significant research articles or information reported appearing on the web.

| deposited research |

Genome Biology used to publish non-peer-reviewed articles in a 'preprint' depository which all individuals can access free of charge. From January 2006 Genome Biology no longer publishes new articles in this section. Authors of articles that were published in this depository have sole responsibility for the article's content; the only screening process used to be to ensure relevance of the preprint to Genome Biology's scope and to avoid abusive, libellous or indecent articles. Articles in this section of the journal have not been peer-reviewed. Each preprint has a permanent URL, by which it can be cited. Research submitted to the preprint depository may have been simultaneously or subsequently submitted to Genome Biology or any other publication for peer review; the only requirement is an explicit citation of, and link to, the preprint in the article that is eventually published. If possible, Genome Biology will provide a reciprocal link from the preprint depository to the published article.

| refereed research |

Genome Biology publishes peer-reviewed research in all areas of molecular, cellular, organismal and population biology that are informed by genomics. All research articles are made available free to individuals through the web, and there are no restrictions on article length or on the types of information that can be included. The publication schedule is fast, using electronic systems for article delivery, proofing and peer-review. The refereed research section includes research, method and software articles

| interactions |

The interactions section includes open letters, correspondence, corrections, discussions and debates. Registered users of Genome Biology may become participants and comment on current trends or specific issues or articles that have appeared in Genome Biology.

| search |

Use the Genome Biology search engine to search our content, search PubMed or search PubMed Central. Genome Biology also offers the option to save and store your searches, and to have the results of searches e-mailed to you at intervals you specify.

| information |

The information section of Genome Biology provides the details of who we are, what the journal aims to offer, a list of our Advisory board, how to submit articles, and how to subscribe or advertise.

Genome Biology article types

Research news

Research news are short news pieces about research articles published in other journals and about events of importance to the scientific community.

Comment

Genome Biology publishes commentaries on a broad range of topics, including political, scientific, and medical issues relating to genomic, post-genomic and genome-scale analyses.

Opinion

Genome Biology publishes opinion pieces, on a broad range of topics, including political, scientific, and medical issues relating to genomic, post-genomic and genome-scale analyses.

Editorial

Genome Biology publishes editorials on a broad range of topics, including political, scientific, and medical issues relating to genomic, post-genomic and genome-scale analyses.

Reviews

Reviews provide include systematic and substantial coverage of material that readers need in order to assess and evaluate progress in genomic and post-genomic research.

Minireviews

Minireviews provide rapid coverage of fast-moving areas, evaluations of progress in specified areas, and critical assessments of emerging technologies.

Tutorials

Tutorials provide 'beginner's guides' to particular tools and resources, aiming to address the questions non-specialists most often want answered.

Protein family reviews

Protein family reviews are structured articles that aim to provide detailed information about an individual family (or subfamily) of structurally and functionally related proteins; each includes information about the characteristic features of family members, from protein structure, function and localization in the cell to gene organization and evolution.

Meeting reports

Meeting reports are short, rapidly prepared and report on recently attended scientific conferences.

Paper reports

Paper reports are short, rapidly prepared and report on recently published research articles. Each report consists of a description of the contents of a particular article, together with a comment on its significance.

Web reports

Web reports are short, rapidly prepared and report on relevant genomic or post-genomic information or tools appearing on the web. Each report consists of a description of the contents of a particular web site, together with a comment on its significance, usability and ease of navigation.

Deposited research

Genome Biology provides a 'preprint' depository which all individuals can access free of charge. Authors have sole responsibility for the article's content; the only screening process is to ensure relevance of the preprint to Genome Biology's scope and to avoid abusive, libellous or indecent articles. Articles in this section of the journal are not peer-reviewed. Research submitted to the preprint depository may have been simultaneously or subsequently submitted to Genome Biology or any other publication for peer review.

Refereed research

Genome Biology publishes peer-reviewed research in all areas of molecular, cellular, organismal and population biology that are informed by genomics.

Finding Genome Biology articles

Customization

We aim to allow you to choose how articles should be listed for you. The key choices you can make about Genome Biology article browsing are:
- view according to subject area or to date of publication
- view more of less detail
- view according to the editors' selection of interesting articles or according to your own saved preferences

Within a section or subsection, the section homepages presents the editor's selection of the most interesting new content within that section. You can choose instead to view all articles within that section sorted by subject or by published date by selecting the relevant option from the navigation menu. (You can make this selection from the navigation bars at any time that you are within the relevant section.)

Tables of contents can be viewed in three different forms: as a list giving the article title, author and published date; as a list giving the full article citation and the subjects in which it is categorized as well as title, author and published date; or as an extended list giving all citation and subject classification information and also displaying the article abstract. To move between these types of display click the 'less detail' and 'more detail' options on the right of the screen. (This option also operates in the gray bar on the right of the homepage.)

Our sections are updated regularly. The most recently published articles are highlighed with a Genome Biology New symbol for not more than two weeks. New articles appear first in tables of contents listings.

Genome Biology subject categories

Genome Biology covers a broad range of scientific topics relating to genomic, post-genomic and genome-scale analyses. Our definitions of specific subject areas aim to help you to find what you are looking for. Let us know if you can't find your biological subject of interest included in this list.

Subject
Definition

Biochemistry and structural biology
Includes biochemistry, biophysics, chemical biology, structure prediction and structure solution, and methods and analysis of proteins, nucleic acids, carbohydrates and lipids, and their metabolism

Bioinformatics
Includes all computational methods, software and models used in the analysis and annotation of sequences, structures and other data

Cancer
Includes cell biological, physiological, clinical and population aspects of cancer

Cell biology
Includes all compartments of the cell and all components of the cytoskeleton, membranes, receptors, cell signalling, cell adhesion, motility and the cell division cycle

Development
Includes all cellular, tissue-level and organismal aspects of plant and animal development

Drug development
Includes pharmacology, pharmaceutics, chemical biology and combinatorial methods, and toxicology, from drug design, through development, to the clinic

Ecology
Includes all aspects of the environmental and population ecology of plants, animals, and microbes

Evolution
Includes molecular evolution and evolution of microbes, plants and animals, as well as phylogenetics and paleontology

Genetics
Includes microbial, plant, animal and human genetic studies, and genetic methods

Genome studies
Includes all genome-scale analyses: genetic and genomic mapping and sequencing, proteomics, microarrays, SNPs, and genomic and post-genomic methods

Immunology
Includes all molecular, cellular and organismal aspects of the immune system, its development, function and evolution

Medicine
Includes all molecular, cellular, organismal and population-level studies relevant to human disease

Methods
Includes methods and methodological innovations from all other subject categories

Microbiology and parasitology
Includes all prokaryotic and eukaryotic microbes and parasites, host responses to them, and antimicrobial drugs

Model organisms
Includes information on laboratory-studied organisms from all other subject categories

Molecular biology
Includes all studies of DNA and RNA in a cellular context: chromatin, transcription, replication, translation, recombination, mutagenesis and DNA repair; as well as recombinant DNA methods and technologies

Neurobiology
Includes all molecular, cellular and organismal aspects of the nervous system, its development, function and evolution

Physiology
Includes molecular, cellular and organismal physiology

Plant biology
Includes all molecular, cellular and organismal aspects of plants, their development, function and evolution

Virology
Includes all studies of viruses, vaccines, antiviral drugs and host responses

Technical issues

Upload

Upload is the Genome Biology system for electronic manuscript subscription. Please note that you must include at least one text (manuscript) file in each submission. If you encounter difficulties using upload, please e-mail the editors giving details of your internet browser and computer specifications (for example, Netscape 4.5 on a Mac using OS 8).

Browsers and monitors

The Genome Biology website is optimized for Microsoft Internet Explorer 4.0 or above, or Netscape Navigator 4.0 or above. We recommend the use of Internet Explorer 5.0 for both Macintosh and PCs and suggest that you use no versions older than Netscape 3.0 or Internet Explorer 3.0 as these will not present the site in full.

The Genome Biology site is designed to look best on monitors set to at least an 800 x 600 resolution and using more than 256 colors. You can edit these settings in the control panel of your computer.

Reprinting article PDF files

Articles can be downloaded and printed as PDF files, which most closely resemble printed journal pages. To view or print PDFs, you need to have Adobe Acrobat Reader installed; if can be downloaded free of charge from the Acrobat website. If you prefer to read them online, you may find it easier if you increase the view size to 125%. If you have difficulty printing a PDF file, try this:

Try printing one page at a time.
Try printing to a newer printer. (Note for Macintosh users: LaserWriter Driver 8.4 may cause some problems.)
Try saving the file to a disk before printing. This requires that you configure your browser to Save rather than Launch Application for the file type application/pdf and can usually be done in the Helper Applications options.
Make sure you are using the latest version of Adobe's Acrobat Reader. You can get this from the Acrobat website [http://www.adobe.com/products/acrobat/readstep.html].
Note for Macintosh users: In order to print files containing large images you may have to increase Adobe's Acrobat Reader memory (select the ~ Adobe's Acrobat Reader icon and change increase the preferred size in File/Get Info/Memory.).
If you are getting Postscript errors on your Macintosh you may have to establish a link of postscript commands between your computer and your printer. Postscript communication on a Mac is handled by a Control Panel called ~ATM (go to System Folder/Control Panels and look for ~ATM). Make sure that you are using the most recent ~ATM version, v4.0 or higher (select the ~ATM icon and check version in File/Get Info). If you do not have ~ATM installed or need a more recent version you can get this from the Acrobat website [http://www.adobe.com/products/acrobat/readstep.html].
If some lines on each page are cut off you may have to change your paper size setting to US letter in File/Page Setup.

About Genome Biology in print

Genome Biology is primarily web-based, but some articles were reproduced in full in a printed issue, and others were reproduced in the print issue in summary form, or listed. The final print issue of Genome Biology was Volume 6 Issue 12 (December 2005); now the journal is published only online. It continues to be published as a monthly issue online (with continuous publication of all articles as soon as they become available) and laid-out PDF versions of all articles continue to be available for downloading from the website. If you have previously been a subscriber to the print version and have questions about converting to an online subscription, please contact our customer services team.

We have a single system for referring to articles, whether they appeared in print or only online, that allows users of traditional citation formats to refer to articles just as easily as those using URLs.

Each article has a unique URL that denotes the year of publication, volume and issue numbers, and its article number within the issue - for example http://genomebiology.com/2003/4/1/202. This URL can be translated into a traditional citation format as follows: Genome Biology 2003, 4:202.

For articles published in volume 3 or earlier, each article has a unique URL that denotes the year of publication, volume and issue numbers, and its article number within a section of the journal - for example http://genomebiology.com/2002/3/2/reviews/0002. This can be translated into a traditional citation format as follows: Genome Biology 2002, 3:reviews0002; if full pages numbers are required they are given in the form reviews0002.1-0002.8

Within each printed issue, you will find articles distributed in sections that mirror those of the website, and the article numbers within a section are not necessarily sequential (if additional intervening article numbers have been used for articles that are published only online). Some articles are incomplete in print.