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Additional files

How to use additional files | Guidelines for specific types of additional file

This page provides information on which formats you should use for specific types of additional files. See the Additional Files Quick Reference for more information.

Additional documentation and Algorithms

Additional documentation and algorithms can be provided in a number of formats, including PDF (Adobe Acrobat), DOC (Microsoft Word), TXT, RTF, EPS, HTML and PPT.

Animations and Movies

Animations can be provided in SWF (Shockwave Flash) format (or converted in a video format).

Movies in mp4, mpeg, mov, avi, swf and animated GIF formats will be embedded in the additional files page. The first frame of the movie will be used as 'poster frame' and will be shown before the user starts movie playback. Other formats will be available for download.

MOV is a common multimedia format, which is often used for saving movies and other video files. This format uses a proprietary compression algorithm developed by Apple Computer; compatible with both Macintosh and Windows platforms. MPG is a common digital video format, which typically incorporates MPEG-1 or MPEG-2 audio and video compression. AVI files can contain both audio and video data in a file container that allows synchronous audio-with-video playback.

Audio

Audio files can be uploaded in a number of formats, including: WAV, MP3, FLAC, AIFF and AU. WAV is a Microsoft and IBM audio file format standard for storing audio bitstreams. It is the main format used on Windows systems for raw and typically uncompressed audio.

Chemical Structures

CDX (ChemDraw) is the file format for saving chemical reaction schemes prepared using ChemDraw. Suggested ChemDraw settings are:

  • Chain Angle 120°
  • Bond spacing 18%
  • Fixed length 0.406 cm (11.5 pt)
  • Bold width 0.056 cm (1.6 pt)
  • Line width 0.018 cm (0.5 pt)
  • Margin width 0.046 cm (1.3 pt)
  • Hash spacing 0.071 cm (2 pt)

TGF (ISIS/Draw) is the file format for saving chemical reaction schemes prepared using ISIS/Draw.

Computational models

We encourage authors to prepare models of biochemical reaction networks using the Systems Biology Markup Language (SBML).

Generic Data Files

DAT (Data file) files are generic data files created by specific applications. They are not an ideal format to use, as they can typically only be accessed by the application that created the file. However, text within DAT files can sometimes be viewed using a text reader.

Geospatial Data

KML (Keyhole Markup Language) is an XML-based language schema for expressing geographic data in two or three-dimensions. KML can be used for geospatial biomedical data suited to 3D spatial visualisation. Google Earth will be used as a viewing application for KML data.

Genomic sequences

Genomic sequences should be formatted according to the Genomic Standards Consortium (GSC) and follow the minimum information about a genome sequence (MIGS) specification. The sequence should be deposited to the International Nucleotide Sequence Database Collaboration (INSDC) prior to submission and the accession numbers provided in the text of the manuscript.

Metabolic networks

Networks can be defined as a collection of interactions between different pairs of nodes. Frequently used formats include KML, BioPax, SBML , PSI-MI, SIF, XML and KGML.

Microarray data

The Minimum Information About a Microarray Experiment (MIAME) or Minimum Information about a high-throughput SeQuencing Experiment (MINSEQE) guidelines should be adhered to when reporting microarray data and we recommend using the spreadsheet-based MAGE-TAB format. We also recommend that you include a copy of the appropriate MIAME checklist.

Mini-websites

Small self-contained websites can be submitted as additional files, in such a way that they will be browsable from within the full text HTML version of the article. In order to do this, please follow these instructions:

  1. Create a folder containing a starting file called index.html (or index.htm) in the root
  2. Put all files necessary for viewing the mini-website within the folder, or sub-folders
  3. Ensure that all links are relative (ie "images/picture.jpg" rather than "/images/picture.jpg" or "http://yourdomain.net/images/picture.jpg" or "C:\Documents and Settings\username\My Documents\mini-website\images\picture.jpg") and no link is longer than 255 characters
  4. Access the index.html file and browse around the mini-website, to ensure that the most commonly used browsers (Internet Explorer and Firefox) are able to view all parts of the mini-website without problems; it is ideal to check this on a different machine
  5. Compress the folder into a ZIP, check the file size is under 20 MB, ensure that index.html is in the root of the ZIP, and that the file has .zip extension, then submit as an additional file with your article

Tabular data

Tabular data can be provided in formats including: DAT, TXT, XLS, CSV, XML and TSV.

See Additional file formats for further information about file formats.

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