Downloading Sequences and Chromatograms

Important Notes

We maintain files on our servers for approximately two months, depending on demand. Please download your sequence files to your own machines to work on them, as files will be purged from the server periodically. We also ask that you disconnect from the server as soon as possible to prevent saturation of our server connections. We maintain backups of all data we generate on CDs.

Please be aware that the text sequence provided to you should be considered 'raw' sequence. It is necessary to view the chromatograms to correct (usually) minor errors and make reasonable judgements of where to trim the sequences. Please look at representative chromatograms here for more information.

Files can be downloaded three ways:
1) Appleshare (Macs mostly--recommended, local or remote access)
2) FTP transfer (best for external or Windows users)
3) Web browser (simplest but some pitfalls).

Appleshare

Open the Chooser, pick Appleshare and connect to the "BSD Learning Center" zone, then choose "Cancer-seqbase" and login using your assigned username and password. Choose the Users drive in the list and click OK. A new colorful icon will appear on the right side of your screen named "Users". Open it and and navigate to your lab's folder and then to your own. Click and drag the appropriate files to your disk. You can view files by date order to assist in picking the most recent files. Please delete old files by throwing them in the trash. A useful shortcut is to make an alias to your lab's folder by selecting it in the Finder and choosing "Make Alias" in the File menu. This alias can then be used to make a faster connection directly to the lab's folder in the future.

FTP transfer

On PC/Macs you need FTP software such as Fetch (Mac) or FTP Explorer (graphical FTP program for Windows 95 or NT 4) or ws_ftp (Windows command line). Connect to "Cancer-seqbase.uchicago.edu" or "CRC-DSF.uchicago.edu" and supply your username and password. Remember to transfer chromatograms as binary files, or use Expander for Windows (see below) to decode the binhex files.

Web browser

For Low Throughput results only, fill out the following form and press submit:
Server machine
Cancer-seqbase.uchicago.edu (internal low throughput users)
CRC-DSF.uchicago.edu (external users)
Username:

For High Throughput results and if you cannot connect using this method (eg. certain web browsers don't automatically request a password), you will need to enter your information manually. Please edit the URL that is pointing to this page in your browser, or choose the option to open a new location and type or paste in one of the following, depending on which server your files are on:

ftp://username:password@cancer-seqbase.bsd.uchicago.edu/     (internal low throughput)

ftp://username:password@CRC-DSF.bsd.uchicago.edu/          (external high & low throughput)

ftp://username:password@DNACore.bsd.uchicago.edu/          (internal high throughput)

A directory listing should appear. If necessary, navigate into the Users directory, then into your lab or institution's directory, and finally into your specific directory. Sequences will be displayed as plain text documents and chromatograms as document files. Click on any file to download it. NOTE! If you only see old files and your new results don't appear, please refresh the page (you may need to hold down the alt/option key too) since web browsers often cache directory views. If they still don't appear, contact us at 773-702-1088.

If the .Seq file appears as a single long string of characters in the Web browser window, you can modify your browser to automatically save it as a text file instead. Open the preferences menu and choose the "Helpers" option (or equivalent). Choose "New" to define a new type, naming it "DNA sequence file", and setting the MIME type to be "TEXT/plain". The suffix should be "Seq". Then choose the handling to be "Save to Disk" and click OK.

Problems

If you encounter problems connecting, viewing or downloading your files, or if you wish to change your password, please contact the Core (773)702-1088.