Don.Gilbert@IUBio.Bio.Indiana.Edu (Don Gilbert) (10/31/90)
The GenBank Search is a Macintosh Hypercard stack for interacting with the computer services of GenBank, the molecular biology databank. The GenBank computer provides two generally useful services for molecular biology by electronic mail: * Searching of the current GenBank databank for similarities with a query nucleic acid or protien sequence of yours, and * Retreival of a sequence in the current GenBank by locus name or accession number. To use this GenBank Search stack, you must have: -- a Macintosh that is connected to the national Internet network, thru an Appletalk or Ethernet cable, -- your Mac must have the MacTCP communications software, and Hypercard version 1.2 or later, from Apple Computer, -- you must have a valid Internet return mail address. This stack includes a simple sequence editor, so you can enter your sequence directly here, and it includes features to read from disk a variety of sequence formats. The Search card then takes whatever sequence you have in the Editor card, bundles that with some information on how to perform the search, and sends it off thru the Internet network using SMTP (simple mail transfer protocol) methods. For the Fetch card, you need to supply an Accession number or GenBank Locus name, which is send off by SMTP to another maildrop at the GenBank computer. GenBank Search stack is available via anonymous FTP to Iubio.Bio.Indiana.Edu, cd [archive.molbio.mac], Get GBSearch.Hqx. This file is a binhex encoding of a stuffit archive of the stack. -- Don Gilbert Don.Gilbert@iubio.bio.indiana.edu biology dept., indiana univ., bloomington, in 47405, usa
lear@turbo.bio.net (Eliot) (10/31/90)
Dave Kristofferson asked me to take a look at your stack, and I found it to be quite nicely done. I'd like to applaud your efforts to improve on the user interface to SEARCH and RETRIEVE. One accesses the GenBank stack as one would any other - by either double clicking on the file, or by jumping to it from Hypercard. The stack then presents you with an introductory display, which is made up of clips from an actual fasta run, I presume. This display also has the author information in it. After a click, a table of contents is presented. The user may access either SEARCH or RETRIEVE from this stack, and it will take data from either a file, or a data card. After collecting all the relevant information, the stack uses XCMDs to talk to MacTCP to communicate with GenBank. The communication, as envisioned by Gilbert, is most amusing to watch. GenBank, pictured as a gargantuan roman building, accepts a beam of light from my little Mac, and the SMTP transaction is mimicked. The results were then processed and returned by GenBank to an account that I specified in the Hypercard stack. Over all, a very nice veneer for the mail system. The one enhancement I would love to see over time would be for the Mac to wait for results from GenBank, and then present them to the user. That's no small task, though. There was one bug in the stack - apparently it only works properly on a Mac II because of the screen size. I don't think this would be a problem if there is a command to turn off the menu bar in Hypertalk. -- Eliot Lear [lear@turbo.bio.net]
gilbertd@silver.ucs.indiana.edu (Don Gilbert) (11/01/90)
In article <1990Oct31.175125.1@csc.fi> harper@csc.fi writes: >the laser from the MAC to the TEMPLE, and the SLOW donkey moving ^^^^^^ Hey, that isn't a monolith or a temple, it is a BANK which i lifted from another hypercard stack (maybe an ancient bank, modern ones look like drive in burger joints). -- don Don.Gilbert@Iubio.Bio.Indiana.Edu biocomputing office, indiana univ., bloomington, in 47405, usa
harper@csc.fi (11/01/90)
In article <7243@cica.cica.indiana.edu>, Don.Gilbert@IUBio.Bio.Indiana.Edu (Don Gilbert) writes: > The GenBank Search is a Macintosh Hypercard stack for interacting with the > computer services of GenBank, the molecular biology databank. The GenBank > computer provides two generally useful services for molecular biology by > electronic mail: I just received GBsearch using another of Don's products HYPERFTP which is a must if you are doing much FTP'ing Just like to report that it fired up no trouble at all... loved the laser from the MAC to the TEMPLE, and the SLOW donkey moving in the background was a nice touch of humour... I set the return address to HARPER@CSC.FI, and believe it or not with FETCH I had just time to walk down the hall from the machintosh room to my own terminal just in time for the mail to arrive back from Genbank. I could imagine a hypercard stack to talk to the BIOSCI nodes at IRLEARN to help people subscribe to lists and more importantly signoff without having to remember all of those queer commands. Thanks once again for a nice programme -=ROB=- P.S. You should copy your note into BIO+SOFT since I am sure lots of people would like to run GBSEARCH on their MAC's
Cherry@Frodo.MGH.Harvard.EDU (J. Michael Cherry) (11/08/90)
In article <1990Oct31.175125.1@csc.fi> harper@csc.fi writes: > I just received GBsearch using another of Don's products HYPERFTP > which is a must if you are doing much FTP'ing The HyperFTP stack was written by Douglas Hornig at Cornell University. See the ? button in HyperFTP for more information. Don Gilbert did modify the HyperFTP stack so that it worked correctly with the VMS directory syntax. > Just like to report that it fired up no trouble at all... loved > the laser from the MAC to the TEMPLE Everyone thinks its a temple. Sure looks like a government bank to me. Mike cherry@frodo.mgh.harvard.edu Department of Molecular Biology Massachusetts General Hospital, Boston 617-726-5955