[Babase] Ranker

Susan Alberts alberts at duke.edu
Thu May 17 12:39:28 EDT 2007


Thanks very much for the helpful feedback Karl. Tyler and Jun, your  
input? I think that from our perspective we would like as many of  
Karl's suggestions as possible to be done before we lose Tyler (and a  
contact email will also be important). But I don't have a sense of  
how much work these represent and what is realistic.
Susan

On May 17, 2007, at 12:23 PM, Karl O. Pinc wrote:

>
> On 05/17/2007 10:43:43 AM, Lacey Maryott wrote:
>> Goodmorning,
>>    I caught up on the e-mails that went back and forth between  
>> Tyler and Karl  last night as well as taking a look at the Wiki to  
>> see the changes.  It looks great, and I see all of the files are  
>> attachments on the Ranker page! Very exciting!
>>    I just wanted to see if anything is needed from us (The Alberts  
>> Lab) at this point.
>> Also, Karl, does this mean that Ranker is officially handed over now?
>
> That's sorta up to our fearless leaders.
>
> I see two things that might need work.  I don't see any copyright
> statements in the code.  And it's not clear to me that you or
> Tabby or whomever can go to the ranker page on the wiki and
> get enough information to install and run the ranker.
> I don't know if you want to tidy this up or make Tyler do it
> or what.  FYI, if you click on the "Attachments" link on the
> ranker page it tells you how to refer to the attachment
> if you want to put a link into the text of the ranker page.
> Seems to me those kinds of links will be necessary.
> "Download *this*, then say 'yes', 'no', 'yes' in answer to
> the installation prompts... etc."
>
> We might want a different page for ranker installation and use
> and ranker code development.  (For that matter we could clean up
> the front page and break it into a couple of smaller pages too
> and otherwise clean up the wiki structure.)
>
> FYIW,
> On the code side of things I've not tried to see if I can
> develop the program futher, setting up the necessary
> environment, seeing what it takes to make the different
> files necessary to install and run the program, and so forth.
> I don't plan on doing so until need be.  At a glance the
> instructions seem sufficient. The one thing I would
> like to see is a version number added to the name of the top
> level directory that holds all the code, so that whoever's
> getting the code can keep track of which version they've got.
> But that's a minor issue not worth holding anything up for,
> and there may be java/Eclipse issues I'm unaware of that
> affect the nameing scheme.
>
> In BabaseRanker/babase/ranker/Database.java I'd like to
> see 172.16.3.1 replaced with papio-vpn.biology.duke.edu,
> but that's trivial.
>
> We should have a contact email for Tyler, just in case.
>
> There's
> also the issue of having to install and start the VPN for those
> not on the Duke network.  Although that also needs review getting
> those instructions clear is not, I think, something that Tyler
> should necessairly be responsible for.  Getting that straightened
> out can go on the Princeton list, or Duke could do it but Duke
> would have to test things from outside the Duke network to be
> sure the instructions work.  I'm sure you'll want to talk to
> me to work through whatever glitches are bound to come up.
>
> Karl <kop at meme.com>
> Free Software:  "You don't pay back, you pay forward."
>                  -- Robert A. Heinlein
>
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-----------------------------------------------
Susan Alberts, Dept. Biology, Duke University, Durham NC 27708. Phone  
919-660-7272, Fax 919-660-7293. alberts at duke.edu



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