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Submitting your manuscript online

PREPARING YOUR MANUSCRIPT

Please ensure that the required formats for text and figure submission are followed strictly.

Word and LaTex templates can be found here. Use of these templates is compulsory.

  1. Follow the instructions to authors regarding the format of your manuscript and references.
  2. For your initial submission, please prepare your manuscript as a single file (a text file with embedded figures, tables etc.), using the appropriate template, as given above. You may either prepare your manuscript using a word processing program and save it as a .doc or .rtf file, remembering to insert your figures and tables into the document. All files in .doc or .rtf format will be converted to .pdf format upon submission. Alternatively, you may prepare your manuscript in LaTeX, and then submit the source files directly as part of your online submission. ScholarOne Manuscripts will then covert them into .pdf format. Because accepted manuscripts are published online following acceptance, it is important that the final version of the manuscript supplied by the author contains no information regarding the citation information (volume, issue, year) or a copyright line as this will mislead readers.
  3. Figures can be saved in .jpg, .gif, .tif or .eps format, at 150 dpi resolution. When preparing figures, please make sure that any characters or numbers included in the figures are large enough to read on-screen.
  4. Prepare any other files that are to be submitted for review, including any supplementary material. The permitted formats for these files are the same as for manuscripts and figures. Other file types, such as Microsoft Excel spreadsheets and Powerpoint presentations may be uploaded but will not be converted to .pdf format. For guidelines on the types of documents that can be uploaded, please click here.
  5. When naming your files, please use simple filenames and avoid special characters and spaces. If you are a Macintosh user, you must also type the three-letter extension at the end of the file name you choose (e.g. .doc, .rtf, .jpg, .gif, .tif, .ppt, .xls, .pdf, .eps, .mov).

SUBMITTING YOUR MANUSCRIPT

Now that your files are ready, visit the online submission web site.

  1. First, you will need to log into the system. Note: Before you begin, you should be sure you are using version 4.0 or higher of Netscape or Internet Explorer. If you have an earlier version, you can download a free upgrade using the icons found at the bottom of our login screen.
    • If you know your login details (i.e. you have submitted or reviewed a manuscript on this system before), use your User ID and Password to log on.
    • If you do not know your login details, check to see if you are already registered by clicking on the 'Check for existing account' button and following the on-screen instructions. If you are not already registered, you can register by clicking on the 'Create a new account' button on the login screen and following the on-screen instructions.
    • If you have trouble finding manuscripts or have other problems with your account do not create another account. Instead, please contact Manuscript Central Customer Support (see below).
  2. To submit a new manuscript, go to the 'Author Centre', choose 'Submit First Draft of a New Manuscript' and then follow the on-screen instructions. There are up to 12 steps for you to follow to submit your manuscript. You move from one step to the next by clicking on the 'Save and Continue' button on each screen or back to the previous screen by clicking on the 'Previous' button. Please note that if you click on the 'Back' or 'Forward' button on your browser, the information you have entered will not be saved. At any stage you can stop the submission process by clicking on the 'Return to Menu' button - everything you have typed into the system up to, but not including, the current screen will be saved. To return to the submission process you will need to click on the manuscript title in the 'Partially Submitted Manuscripts' section in your 'Author Centre'. You may like to have the original word processing file available so that you can copy and paste the title and abstract into the required fields.
  3. To upload your files in the Author Centre 'File Upload Centre':
    • Click on the 'Browse' button and locate the document you want to upload.
    • Select the document's designation from the pull-down menu. The designation choices may vary from journal to journal, but will always include 'Main Document' (your manuscript text).
    • You will also be asked whether each document you upload should be considered for review, and the default is set to 'Yes'. Please be advised that, if you select 'No', the editorial staff will still be able to view that document and make it available to an editor or reviewer if necessary.
    • Click on the upload button to submit your file. If you are uploading your manuscript file, and it is in one of the formats specified above, it will be automatically converted to a .pdf file for peer review.
    • When the upload of each file is completed, you will see a confirmation window asking you to write a description of that document. For your Main Document, you can use language such as 'Manuscript Text' or 'Main Document'. For any figures that you need to upload separately, please include the figure number, e.g. 'Figure 1' or 'Fig. 1'. For any other supporting documents, please indicate clearly what the document is as well as its format (MS Excel, MS Word, etc.).
  4. From the files you submit to make up your manuscript, the system creates and stores separately two types of documents:
    • Files for Review. These will be the files viewable to the editor and reviewers of your manuscript. The system will automatically convert your text documents (any document in .doc or .rtf format) into .pdf and make that newly converted document accessible for review, leaving the originally uploaded document under the second column, 'Files for Production'. [Note: PDF files are readable with Adobe Acrobat Reader, available for download from the main login screen of Manuscript Central, as well as from www.adobe.com.] The system will also convert and save under 'Files for Review' all files with images (figures, charts, graphs, etc.) in.jpg, .gif, .tif and .eps format, converting them into smaller .jpg images, leaving the original files under 'Files for Production'. The smaller versions of your image will include in the filename '_sm.jpg'. The system will also save under 'Files for Review' any documents which are uploaded in formats that it cannot convert.
    • Files for Production. These are all the original word-processor files and figures you uploaded. Not listed here will be those files you designated for review but submitted in a format that cannot be converted by the system.
  5. After the successful upload of your text and images, it will be possible for you to view and proof your manuscript now located on the web site. The on-screen version of your manuscript you review at the journal's web site will also be the version accessed by the editor and the reviewers.
  6. If the files have not been uploaded to your satisfaction, click on the 'Previous' button to move back to the file upload screen where you can remove the files you do not want, and repeat the upload process.
  7. When you are satisfied with the uploaded manuscript then click on the 'Submit' button. It is not until this button is pushed that the manuscript and all of the associated information (i.e. contributing authors, institutions, etc.) is linked together and the manuscript is given a manuscript number. Once the manuscript is submitted it is not possible to undo the submission.
  8. After the manuscript has been submitted you will receive an email confirmation stating that your manuscript was successfully submitted. This email will also give the assigned manuscript number, which is used in all correspondence. If you do not receive this email, your manuscript will not have been successfully submitted to the journal and the paper cannot progress to peer review. If this is the case your manuscript will still be sitting in the 'Partially Submitted Manuscripts' section of your 'Author Centre' awaiting your attention.
  9. If you return to your 'Author Centre' you will notice that your newly submitted manuscript can be found in the 'Submitted Manuscripts' area. Among the information listed there, the 'Processing Status' section provides information on the status of your manuscript as it moves through the review process.

SUBMITTING A REVISED MANUSCRIPT

  1. Logon to the online submission web site as before and, in the 'Author Centre', click on 'Manuscripts to be Revised'. You will then see the title of any manuscripts you submitted that are under revision.
  2. If you click on the manuscript title you will reach the 'File Manager' screen. Here you can upload the files that constitute your revised manuscript. To facilitate the production process, it is ESSENTIAL that you upload the following revised manuscript files at the revision stage:
    • EITHER:: (i) A .doc or .rtf file of the revised manuscript, with all tables, figures, schemes and equations inserted in the document.
    • OR: (ii). All necessary LaTeX files that will be required by the typesetter (including bib, .bst and .ps files), along with postscript and PDF versions of the complete manuscript.

    Please note that the publication of your manuscript will not proceed until all of the necessary files are received.
    If you decide to mark-up the changes made after revision, please only do this by using the track changes function or highlighting these in red text

  3. If you click on 'View comments/respond' you will see the editor's letter to you together with the referees' comments. You may cut and paste your responses into the text areas at the bottom of the screen.

Getting help
If you experience any problems during the online submission process please use the 'Author Help' function, which takes you to specific submission instructions, or 'Get Help Now', which takes you to the Frequently Asked Questions page. Alternatively, contact the Editorial office at bioinformatics.editorialoffice@oup.com