Dear Software Communauty support, I am a member of the Debian-Med project, and would like to enquire about two related questions:
1) The definition of a MIME type for .ab1 files. 2) The auto-detection of ABIF chromatograms. In the Debian-Med project [1], our goal is to provide and integrate free software for medical practice and life science research. We are currently working on associating file types to the applications that can open them, so that our users can have a desktop environment in which a double-click will work without post-installation configuration. [1] http://www.debian.org/devel/debian-med The EMBOSS software suite provides `abiview' [2], a program to display chromatograms in ABIF format. On desktop systems complying to the FreeDesktop standards, applications are associated to MIME types [3], and files are associated to MIME types independently [4]. [2] http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/abiview.html [3] http://standards.freedesktop.org/desktop-entry-spec/latest/ [4] http://standards.freedesktop.org/shared-mime-info-spec/latest/ ABIF-formatted chromatograms have not officially defined mime types. Some labs use application/abi1 [5] or application/x-dna [6], but the first violates the standards [7], and the second is using a very generic name. According to the section 2.1.2 of the standard, we would like to use a type like `application/vnd.appliedbiosystems.ab1' or something similar. We would like to have your approval before using such MIME types. Also, if you find the idea interesting, it may be useful to properly register them. [5] http://gatc.arl.arizona.edu/resources/faqs/sequencing/view.php [6] http://bioinformatics.unc.edu/software/sequencher/seq_ABI_files_mac.htm [7] http://www.ietf.org/rfc/rfc2048.txt The second half of the file—application association is the auto-detection of the file MIME type. This is done by two ways: from the suffix and from the contents. For the suffix, we are lucky that .ab1 is not used by other applications. For the contents however, we did not manage to unequivocally detect chromatograms in ABIF format [8], because we did not manage to find a simple way to differentiate them from the ABIF-formatted fragment analysis files (.fsa) produced by your instruments. [8] http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf To detect the ABIF format, we detect the character chain `ABIF??tdir' (ignoring the characters where the question marks are) at the head of the file. Can you indicate us if there is a specific chain that distinguishes the chromatograms from the fragments analysis files, at a given offset in the ABIF-formatted files ? This email is copied to our mailing-list, as a continuation of our discussion on this subject [9]. But do not hesitate to answer only in private if you prefer. [9] http://lists.debian.org/debian-med/2008/01/msg00135.html Best regards, -- Charles Plessy Debian-Med packaging team http://www.debian.org/devel/debian-med Wakō, Saitama, Japan -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
