Parasite genome databases and genome research resources


[ ACEDB | PERL | LINUX | GAWK | HTML | WWW ]

Where to get software and databases on the internet.
Still under construction...

For general molbio things, here's a link to the Biologist's Control Panel page maintained by the Baylor College of Medicine Genome Center

You could also try Sanger Centre Quick Guide to Internet Resources, Pedro's Biology Research Tools, NIH (National Institutes of Health) Home Page, or Molecular Biology WWW Servers in the World


ACEDB

  • ACeDB for UNIX

  • ACeDB for LINUX

  • MacACE

  • C. elegans ACeDB

  • C. elegans ACeDB for Mac

  • Other ACE Genome Databases

  • ACEDB Developers conference documents

    For the latest "Frequently Asked Questions" about ACeDB, including the latest lists of what db are available where try the ACeDB FAQ List at NAL

    PERL

    LINUX

    GAWK

    HTML editors

    Web Browsers and supporting applications


    ACeDB for UNIX: ACeDB version 4

    written by R. Durbin and J. Thierry-Mieg
    Currently version 4.3
    Version 1 was the original C. elegans database
    Version 2 was the all singing all dancing C. elegans database and
    Version 3 was a blank engine ready for anyone to port any data into.

    Version 4.3 available for all Unix systems by anonymous ftp at :-

    In the UK ftp.sanger.ac.uk/pub/acedb/ace4_3/ (NOTE No version 4.3 for Linux here)

    In the US ncbi.nlm.nih.gov/repository/acedb/ace4_3/

    In France lirmm.lirmm.fr/pub/acedb/ace4_3/ (NOTE No version 4.3 for Linux here)

    In Israel bioinformatics.weizmann.ac.il/pub/databases/acedb/ace4_3/ (NOTE No version 4.3 for Linux here)


    LINUX compiled ACEDB 4.3

    Version 4.3 of Acedb for Linux is available from the following sites :-

    In the US ncbi.nlm.nih.gov/repository/acedb/ace4_3/

    In the UK ftp.ebi.ac.uk/pub/databases/parasites/bin/


    MacACE

    This is the Macintosh version of the database for the C. elegans genome sequencing project ACeDB ( A C. elegans Data Base), written by R. Durbin and J. Thierry-Mieg. This is a port of the Unix database by Frank H. Eeckman and Cyrus Harmon

    MacAce 2 and MacAce4.04b (a beta release) as "standalone" or "empty" versions are available at the same sites in both a PowerPC version and a "fat" binary version for 030/040 Macs
    available by anonymous ftp at

    genome.lbl.gov in /pub/macace
    and
    ftp.sanger.ac.uk/pub/acedb/macace


    C. elegans ACeDB


    a message from the C. elegans ACeDB developers posted to the C. elegans newsgroup:

    (NOTE The updates are now subdivided into one set (update.WG1.4-1.tar.Z etc.) without the full nucleotide data and another set (update.WS1.4-1.tar.Z etc.) with nucleotide data. The former set is currently (10/10/96) at release 4-6 whereas the latter (much much larger in size) is at release 4-20. The method for uploading and installing remains the same however - although version 4_3 of the ACEDB code should be used.)

    ACEDB data updates 4-1 to 4-6 for C. elegans

    There is a new version of the C. elegans ACEDB database. This uses version 4_0 of the ACEDB code (subversion beta4). There will be a separate email message about the code for those using ACEDB for other organisms. To build the C. elegans database you will need to get all six update files update.4-1.tar.Z to update.4-6.tar.Z.

    The total database size is now approximately 160Mbytes. As well as a large amount of new sequence data, this contains all the genetic mapping data submitted to the CGC in Cambridge up to April 1995, together with a draft new map, and the abtracts for the 1995 Worm Meeting with links to Gene, Rearrangement and Sequence objects.

    This release is fully up to date with respect to the physical map, the CGC information, and gene/genetic map information prior to that resulting from the recent call for data (which we are working on now). We have also added over 200 Medline references and a significant number of missing Gazette pages. There is also a lot of new genomic sequence information.

    Instructions for obtaining updates/the whole thing
    All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet:

    ncbi.nlm.nih.gov (130.14.20.1)

    in the USA, in repository/acedb/celegans

    and from

    sanger.ac.uk

    in England, in pub/acedb/celegans

    lirmm.lirmm.fr (193.49.104.10)

    in France, in directory genome/acedb/celegans

    In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource.

    Example:

    ftp ncbi.nlm.nih.gov
    login: anonymous
    password 'your email address'
    cd repository/acedb/ace4
    binary
    mget *
    get README y/n answer yes etc
    ...
    ...
    quit

    Get all the update.4-n.tar.Z and read the files README and NOTES before proceeding further.

    Always get a copy of the INSTALL script. Move it and the .tar.Z files into the home directory in which you are installing ACEDB. Type "source INSTALL". Start acedb (normally by typing "acedb") and choose "Add Update File" from the menu (right button), and press "All updates" with the left mouse button.

    If you have a problem making the program work, look at the section on problems in NOTES, and if that fails to help, let us know.

    Please send any comments, especially about anything you think is wrong to one of us:

    Richard Durbin (rd@sanger.ac.uk) Sylvia Martinelli (sylvia@sanger.ac.uk)


    C. elegans ACeDB for Mac


    MacAce 2 and macAce4.04b are available as complete C. elegans databases from
    genome.lbl.gov
    and
    ftp.sanger.ac.uk/pub/acedb/macace


    other versions of ACeDB


    A link to a copy of the Databases at NAL page

    PERL

  • MacPerl

  • UNIX Perl


    Perl is a programming language similar in many ways to C and of great use for manipulating files of text based data from one format to another.

    Recommended literature :-

  • For beginners, Learning Perl (Randal L. Schwartz, publ. O'Reilly and Associates inc.)

  • More advanced, Programming Perl (Larry Wall and Randal L. Schwartz, publ. O'Reilly and Associates inc.)

    MacPerl

    by Matthias Neeracher and Tim Endres .
    "It runs every program in the test suite that you could it reasonably expect to, and some you probably didn't expect. Feel free to give this program away according to the terms stated in the README file."

    get it from:
    In the UK, sunsite.doc.ic.ac.uk/packages/mac/applescript/scripts/MacPerl

    In Switzerland, nic.switch.ch/software/mac/perl

    In the US, ftp.duke.edu/.1/perl/ports/mac/

    In Germany, ftp.ipc.uni-tuebingen.de/mirrors/CPAN/ports/mac/

    This package contains a compiler and various libraries that should have everything in them you need.

    The current distribution consists of the following files:

    Mac_Perl_412_appl.sit.bin The standalone application
    Mac_Perl_412_tool.sit.bin The MPW tool
    Mac_Perl_412_src.sit.bin Perl sources

    The following are also linked into Perl
    GUSI_135.sit.bin Socket library
    XL_10.sit.bin XCMD/XFCN library
    db_16m2.sit.bin Berkeley dbm library

    Mac_Perl_appl.sit.bin and Mac_Perl_tool.sit.bin always point to the latest version of these files.


    UNIX PERL

    The source code for Perl for Unix systems is available from ftp many sites, the following sites are just a few examples :-

    In the UK, src.doc.ic.ac.uk/pub/packages/perl/perl.5.0/

    In the US, cs.oswego.edu/pub/Z/gnu/

    In the US, labrea.stanford.edu/pub/gnu/

    In Germany, ftp.uni-magdeburg.de/pub/mirror/freebsd/distfiles/


    LINUX

    Linux is 'Unix for the PC'. It can run on a relatively small PC (386) although the faster processor, bigger hard disk and more RAM the better. It is generally freelly available, either :-

  • On CD-ROM - several versions are available by mail order for a small charge (usually to cover postage and cost of the CD, check the small ads in one of the numerous monthly PC magazines) and also free with Linux textbooks (check your local academic bookstore) and occasionally on the free cover CD-ROMs given away with magazines (albeit in a stripped down version).

  • Via anonymous ftp - Linux is available via ftp from several sites. In general terms, the ftpable version of Linux is setup to be downloaded floppy disk by floppy disk and then installed via floppy (patience is required as it can reach over 50 disks if most of the options are required). Check the documentation at the ftp sites listed for more detail on how to get and install Linux from floppies via anonymous ftp :-

    In Germany, ftp.rz.uni-wuerzburg.de/pub/linux/slackware/

    In the UK, sunsite.doc.ic.ac.uk/pub/packages/Linux/slackware-3.1/

    In the US, sunsite.unc.edu/pub/Linux/distributions/slackware/

    Follow this link for

    ACeDB for LINUX

    If you know of other resources which should be listed here please email me:

    aslett@ebi.ac.uk



    GAWK

    Gawk is the GNU implementation of Awk, another language designed for handling data-reformatting simply with a few lines of code. See The GAWK manual for further details. As with Perl,, Gawk is available from numerous ftp sites. Here are a few of them :-

    In the UK, sunsite.doc.ic.ac.uk/Mirrors/ftp.cdrom.com/pub/FreeBSD/distfiles/

    In the US, cs.oswego.edu/pub/Z/gnu/

    In the US, labrea.stanford.edu/pub/gnu/

    In Germany, ftp.uni-magdeburg.de/pub/mirror/freebsd/distfiles/

    If you know of a resource which should be listed here please email me:

    aslett@ebi.ac.uk



    HTML_editors

    This site has details of editors and other WWW tools, http://www.w3.org/hypertext/WWW/Tools/Overview.html#he1


    If you know of a resource which should be listed here please email me:

    aslett@ebi.ac.uk



    Web Browsers


    The three most widely used browsers are :-

    Netscape - http://home.netscape.com/

    Microsoft Internet Explorer - http://www.microsoft.com/

    Mosaic

    If you know of a resource which should be listed here please email me:

    aslett@ebi.ac.uk

    last changed 10/10/96