dna106 | 16 Oct 05:52 2002
Picon

[BioPython] download

dear all:
    I try to download from http://www.biopython.org/Download/
,but it can't get link.
Is it ok ?
Thanks a lot!
 
This is kenny
Jeffrey Chang | 16 Oct 07:23 2002
Picon

Re: [BioPython] download

Hi Kenny,

There have been a lot of network changes in the last week or so, so
it's possible something got broken in the move.  I'll check on it
tomorrow.  Sorry about the inconvenience.

Jeff

On Wed, Oct 16, 2002 at 11:52:09AM +0800, dna106 wrote:
> dear all:
>     I try to download from http://www.biopython.org/Download/
> ,but it can't get link.
> Is it ok ?
> Thanks a lot!
> 
> This is kenny
_______________________________________________
BioPython mailing list  -  BioPython <at> biopython.org
http://biopython.org/mailman/listinfo/biopython

Jeffrey Chang | 17 Oct 05:28 2002
Picon

Re: [BioPython] download

Things should be working again.  Please let me know if there are any
further problems.

Jeff

On Wed, Oct 16, 2002 at 11:52:09AM +0800, dna106 wrote:
> dear all:
>     I try to download from http://www.biopython.org/Download/
> ,but it can't get link.
> Is it ok ?
> Thanks a lot!
> 
> This is kenny
_______________________________________________
BioPython mailing list  -  BioPython <at> biopython.org
http://biopython.org/mailman/listinfo/biopython

Patrick K. O'Brien | 18 Oct 15:53 2002

[BioPython] Python for Bioinformatics article

I'd like to thank everyone on this list that reviewed my Beginning Python for 
Bioinformatics article. Your feedback was very helpful, even when I wasn't 
able to incorporate every suggestion. I do hope the article helps expose more 
bioinformatics folks to my favorite language. You can see the final, 
published version on the O'Reilly website:

http://www.onlamp.com/pub/a/python/2002/10/17/biopython.html

Thanks again,

Pat

--

-- 
Patrick K. O'Brien
Orbtech      http://www.orbtech.com/web/pobrien
-----------------------------------------------
"Your source for Python programming expertise."
-----------------------------------------------

_______________________________________________
BioPython mailing list  -  BioPython <at> biopython.org
http://biopython.org/mailman/listinfo/biopython

Ravinder Singh | 22 Oct 17:16 2002
Picon

[BioPython] Promotional Ads

Dear Biopython community,
I hope most of us agree that in today's world there is no dearth of
getting unsolicited ads or e-mails. When I joined the biopython's
mailing list, I didn't anticipate that my subscribing to this will open
yet another door to receive junk mail; I'm referring to for example
those advertising Shoe soles etc. from China.  Of course, I enjoy being
part of the biopython community, but I'd appreciate if I could be saved
from unnecessary advertising..
Many thanks if you are able to do something about it.
Ravinder

--
********************************************************************************

Dr. Ravinder Singh
Assistant Professor
MCD Biology
347 UCB
University of Colorado
Boulder, CO 80309-0347

(303)492-8886 (voice)
(303)492-7744 (fax)

_______________________________________________
BioPython mailing list  -  BioPython <at> biopython.org
http://biopython.org/mailman/listinfo/biopython

David A. Jewell | 22 Oct 17:31 2002

Re: [BioPython] Promotional Ads

Dr. Singh sentiments are my own and I would very much appreciate
efforts in securing the Bio-python server from what appears
to be frequent hacks.

Thank you,
David Jewell
Research Computing
Dartmouth College

--- Ravinder Singh wrote:
Dear Biopython community,
I hope most of us agree that in today's world there is no dearth of
getting unsolicited ads or e-mails. When I joined the biopython's
mailing list, I didn't anticipate that my subscribing to this will open
yet another door to receive junk mail; I'm referring to for example
those advertising Shoe soles etc. from China.  Of course, I enjoy being
part of the biopython community, but I'd appreciate if I could be saved
from unnecessary advertising..
Many thanks if you are able to do something about it.
Ravinder
--- end of quote ---
_______________________________________________
BioPython mailing list  -  BioPython <at> biopython.org
http://biopython.org/mailman/listinfo/biopython

Danny Yoo | 22 Oct 19:17 2002
Picon

Re: [BioPython] Promotional Ads


On 22 Oct 2002, David A. Jewell wrote:

> Dr. Singh sentiments are my own and I would very much appreciate efforts
> in securing the Bio-python server from what appears to be frequent
> hacks.

How about if the biopython lists are restricted so that only subscribers
can post?  This is the approach that many other Mailman mailing lists have
taken to prevent junk mail from flooding the list.

It's also extraordinarily disheartening when there's more spam than actual
bug reports in Jitterbug; I personally almost despise getting mail from
biopython-dev simply because it's spam for the most part!

The mailing lists on mail.python.org also have a spam filter that seems to
be fairly effective.  Someone may want to contact the mail.python.org
administrator and see if a similar system can be set up for Biopython.org.

_______________________________________________
BioPython mailing list  -  BioPython <at> biopython.org
http://biopython.org/mailman/listinfo/biopython

Chris Dagdigian | 22 Oct 19:28 2002

Re: [BioPython] Promotional Ads


These complaints should have been sent to the OBF sysadmin team 
(root-l <at> bioperl.org) so we could have responded. I can't subsribe to 
every one of our 35+ lists you know :)

I've set up more restrictive anti-spam rules within Mailman for both the 
bioperl and biojava mailing lists. The lists still allow outsiders to 
post but we hold-for-moderation all emails that are not mime-encoded as 
text/plain and any emails that include attachments. This works very well 
but places an administrative burden on our volunteer mailing list 
moderators.

The BioMoby list has taken this even futher-- they have elected to close 
the list to outside posters -- all posts from non-members are held for 
moderation and the moby list members have stepped forward to handle the 
moderation tasks.

We also subscribe on a server level to the http:///mail-abuse.org RBL+ 
blackhole list which allows us to refuse inbound SMTP connections from 
IP addresses of known spammers or open relays. Sadly this filter has not 
worked since we changed IP addresses a few weeks ago. We have an open 
ticket in with mail-abuse.org to update their databse with our new IP.

So- please discuss amongst yourselves what additional steps you'd like 
to take. I'd recommend trying to block all attachments and non-plaintext 
emails before  taking the more drastic step of taking the list private. 
It would also help greatly if there were a member or two on this list 
who would volunteer to join our mailteam to help with the increased 
moderation duties.

Regarding jitterbug -- you can elect to disable the email-based bug 
reporting or you can switch to Bugzilla as bioperl did. In fact I think 
Jeff has already set up bugzilla for biopython?

Regards,
Chris
Open-Bio.org

Danny Yoo wrote:

>On 22 Oct 2002, David A. Jewell wrote:
>
>  
>
>>Dr. Singh sentiments are my own and I would very much appreciate efforts
>>in securing the Bio-python server from what appears to be frequent
>>hacks.
>>    
>>
>
>
>How about if the biopython lists are restricted so that only subscribers
>can post?  This is the approach that many other Mailman mailing lists have
>taken to prevent junk mail from flooding the list.
>
>It's also extraordinarily disheartening when there's more spam than actual
>bug reports in Jitterbug; I personally almost despise getting mail from
>biopython-dev simply because it's spam for the most part!
>
>
>The mailing lists on mail.python.org also have a spam filter that seems to
>be fairly effective.  Someone may want to contact the mail.python.org
>administrator and see if a similar system can be set up for Biopython.org.
>  
>

_______________________________________________
BioPython mailing list  -  BioPython <at> biopython.org
http://biopython.org/mailman/listinfo/biopython

James Freeman | 24 Oct 13:46 2002
Picon

Re: [BioPython] Promotional Ads

Hi Chris,

If they take the DAS route, members only, with non member mail being 
cleared by a several volunteer spam filters (I am one of four volunteers 
for DAS).  The spam goes to nothing, I can't block a valid mail without 
all the other mail admins knowing about it.  A couple of minutes a day 
is all that is needed.  The DAS lists spam has dropped to nothing since 
then, and I have sent through several pieces of relevant non-member 
mail.  So if they do that sign me up.

Warmest Regards,

Jim Freeman
Bioinformatics Consultant At Biogen

Chris Dagdigian wrote:

>
> These complaints should have been sent to the OBF sysadmin team 
> (root-l <at> bioperl.org) so we could have responded. I can't subsribe to 
> every one of our 35+ lists you know :)
>
> I've set up more restrictive anti-spam rules within Mailman for both 
> the bioperl and biojava mailing lists. The lists still allow outsiders 
> to post but we hold-for-moderation all emails that are not 
> mime-encoded as text/plain and any emails that include attachments. 
> This works very well but places an administrative burden on our 
> volunteer mailing list moderators.
>
> The BioMoby list has taken this even futher-- they have elected to 
> close the list to outside posters -- all posts from non-members are 
> held for moderation and the moby list members have stepped forward to 
> handle the moderation tasks.
>
> We also subscribe on a server level to the http:///mail-abuse.org RBL+ 
> blackhole list which allows us to refuse inbound SMTP connections from 
> IP addresses of known spammers or open relays. Sadly this filter has 
> not worked since we changed IP addresses a few weeks ago. We have an 
> open ticket in with mail-abuse.org to update their databse with our 
> new IP.
>
> So- please discuss amongst yourselves what additional steps you'd like 
> to take. I'd recommend trying to block all attachments and 
> non-plaintext emails before  taking the more drastic step of taking 
> the list private. It would also help greatly if there were a member or 
> two on this list who would volunteer to join our mailteam to help with 
> the increased moderation duties.
>
> Regarding jitterbug -- you can elect to disable the email-based bug 
> reporting or you can switch to Bugzilla as bioperl did. In fact I 
> think Jeff has already set up bugzilla for biopython?
>
> Regards,
> Chris
> Open-Bio.org
>
>
>
> Danny Yoo wrote:
>
>> On 22 Oct 2002, David A. Jewell wrote:
>>
>>  
>>
>>> Dr. Singh sentiments are my own and I would very much appreciate 
>>> efforts
>>> in securing the Bio-python server from what appears to be frequent
>>> hacks.
>>>   
>>
>>
>>
>> How about if the biopython lists are restricted so that only subscribers
>> can post?  This is the approach that many other Mailman mailing lists 
>> have
>> taken to prevent junk mail from flooding the list.
>>
>> It's also extraordinarily disheartening when there's more spam than 
>> actual
>> bug reports in Jitterbug; I personally almost despise getting mail from
>> biopython-dev simply because it's spam for the most part!
>>
>>
>> The mailing lists on mail.python.org also have a spam filter that 
>> seems to
>> be fairly effective.  Someone may want to contact the mail.python.org
>> administrator and see if a similar system can be set up for 
>> Biopython.org.
>>  
>>
>
>
> _______________________________________________
> BioPython mailing list  -  BioPython <at> biopython.org
> http://biopython.org/mailman/listinfo/biopython
>

_______________________________________________
BioPython mailing list  -  BioPython <at> biopython.org
http://biopython.org/mailman/listinfo/biopython

Andreas Kuntzagk | 24 Oct 16:18 2002
Picon

[BioPython] GenBank.FeatureParser and multiple accessionnumbers

Hi,

at the moment the GenBank.FeatureParser stores only the first accession
number of an entry. (right?)
Would it make sense to store all of them? (e.g. as an annotation)
I would like to search a dictionary of SeqRecords by an accession
number. 

ciao, Andreas "murple" Kuntzagk

--

-- 
Andreas Kuntzagk <andreas.kuntzagk <at> mdc-berlin.de>

_______________________________________________
BioPython mailing list  -  BioPython <at> biopython.org
http://biopython.org/mailman/listinfo/biopython


Gmane