[Bioperl-l] problem to fit genomic coordinates

Mark A. Jensen maj at fortinbras.us
Thu Mar 26 15:17:22 EDT 2009


I know that enough has been said on this issue, but I want
to address not only you but all the student lurkers on the
list. bioperl-l is mainly a place for professional questions
and answers, but there is a very strong educational
component here as well. That comes directly from the
attitude of the BioPerl leadership, who are mainly academic
in origin, who love to program and to teach programming. The
ethic "we don't do homework for you" is really part of that
educational mission that is subconsciously built in to

It is a really, really serious mistake to treat global
experts in a field you're interested in entering as if they
owed you something. On the contrary, every help response to
this list is time, worth hundreds of euros an hour, given
away for free. The motivations for giving it vary, but the
fact that it deserves gratitude and attentiveness does
not. You will be very hard-pressed to find a listserv as
helpful as this, not to mention as forgiving. Other places
would have banned you instantly; instead, at the end of your
tirade you received several patient and helpful responses.

I have thought for a long time (and I've been in the biz a
long time) that students need to attempt to forget that they
are students, and start imagining themselves as scientists
right now where they are. Leave behind the mindset that
you're just trying to make it through another course, and
adopt the mindset that you are preparing yourself to pursue
something you love to do. Until this happens, you are not a
professional, you don't think like professional, and you're
liable to make serious mistakes. Scientists are very social,
and have very long memories. Those two qualities make them
good scientists. However, those qualities can also make it
very difficult to reinvent yourself in their minds, if you
screw up. You have to work very, very hard to overcome it.

So, in the future, think of yourself as a scientist, in a
community of scientists, each of whom could be helpful and
useful to you. They will then think of you that way too, and
it will help you do what you want to do. Good luck-


----- Original Message ----- 
From: "Laurent MANCHON" <lmanchon at univ-montp2.fr>
To: "Chris Fields" <cjfields at illinois.edu>; <bioperl-l at lists.open-bio.org>
Sent: Thursday, March 26, 2009 11:30 AM
Subject: Re: [Bioperl-l] problem to fit genomic coordinates

okay, you are right,
but i think in my opinion that my question is a good question about
parsing enormous
range of intervals.
The problem is not perl, bioperl, or other language, it's just an
algorithmic question.
I'm not a professionnal in Bioperl and i don't know what is possible to
do with all the Bioperl modules.
So if you think it's possible to resolve my question with Bioperl maybe
you are right, but in my position i stay in the same point.
If you want i send you the two files needed in my question. And if you
are agree try to use Bioperl to resolve it. Maybe it's not possible because
files are big, i don't know.

Chris Fields a écrit :
> (edited for those with sensitive eyes)
> Laurent,
> Please keep all responses, no matter how puerile, on the mail list ;>
> We're trying to point out the blatantly obvious: this isn't the place for your 
> question.  Sorry if that irritates you.  And, to reiterate, don't be surprised 
> if you get some nasty responses.
> chris
> (hoping this isn't one of the GSoC students, as he's introducing Laurent to 
> his spam filter)
> On Mar 26, 2009, at 10:04 AM, Laurent MANCHON wrote:
>> p*** off
>> Chris Fields a écrit :
>>> On Mar 26, 2009, at 8:36 AM, Laurent MANCHON wrote:
>>>> Chris Fields a écrit :
>>>>> On Mar 26, 2009, at 3:31 AM, Laurent MANCHON wrote:
>>>>>> yes but this is a school problem that my teacher ask us to resolve 
>>>>>> without using Bioperl modules !
>>>>> I didn't bother reading beyond that sentence.  Not to state the absolute 
>>>>> obvious here, but:
>>>>> 1) you are posting to the bioperl list for a non-bioperl-related question, 
>>>>> and
>>>> genomic coordinates are not questions about biology ?
>>>> i'm speaking about GENOME, and not GEOGRAPHY
>>> And this is a mail list for BioPerl (the toolkit), not perl and biology.  We 
>>> will sometimes answer questions along these lines if they are relevant, but 
>>> apparently our answers (all notably BioPerl-related, mind you) were tossed 
>>> to the side and you asked for more.
>>> I suppose you at least showed some honesty and revealed exactly why you 
>>> needed this answered, but again, don't be surprised if you get a nasty 
>>> response and no answers.  You won't get any from me.
>>>>> 2) you are committing one of the biggest no-no's for a list, asking us to 
>>>>> help you with your homework.
>>>> in bioperl you have BIO, okay but too you have PERL !
>>> Interesting how you skirted that last question.  We won't do your homework 
>>> for you.  Sorry.
>>> chris

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