Re: Documentation, tutorials and cookbook about pairwise sequence alignment

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Hi Andreas.

Thank you very much for the fixes. Surely it will help me.
I have understood the problem you encountered with the old site.
Now I will try to apply those things.

Thanks again,
Andrea

2016-05-23 19:27 GMT+02:00 Andreas Prlic <[email protected]>:

> Hi Andrea,
>
> Sorry for the inconvenience. We had to turn the old site off, since there
> were too many security breaches which resulted in content spamming. This is
> across all bio* projects...
>
> I fixed the links on the CookBook4 page. Checking some of the related
> pages, there are still a lot of formatting issues. That will take a bit to
> fix them all up. However, each page at the bottom has an "edit this page"
> link, which makes it easy to access the raw markdown content.  It is
> possible to see the code in a more readable way. I also fixed up this page
> for now: http://biojava.org/wikis/BioJava:CookBook3:PSA/
>
> Hope that helps,
>
> Andreas
>
>
>
> On Sat, May 21, 2016 at 4:09 AM, Andrea Battistelli <
> [email protected]> wrote:
>
>> Hello everyone.
>>
>> I have been studying the pairwise sequence alignment concept for a
>> project that I need to do for an exam.
>> In particular I am interested in the global and local alignments and all
>> the things related to them (how they are implemented, how I can generate a
>> paiwise alignment, ect.).
>> I would implement my project in Java employing indeed BioJava as starting
>> point.
>> I set up correctly the Maven project on Eclipse so no problem under that
>> point of view.
>>
>> Few months ago I have seen there was all the documentation, tutorials and
>> specifications about the BioJava project based on the Wiki pages.
>> I have seen it has been all migrated into a new web site but now I am not
>> finding any documentation, tutorial or cookbook about the topic of personal
>> interest.
>>
>> - In the BioJavaTutorial page - book 2, the alignment module has no pages
>> of explanation.
>> - In the CookBook4.0, all the links relative to the paiwise sequence
>> alignment give me back an "address uninterpretable" message.
>> - Finally in the Wiki Pages section there are many links. In some of
>> these there are links interesting for me but they contain not well
>> formatted codes.
>>
>> I know that it may taketime to migrate all the things but in the meantime:
>> Is there any possibility to have the reference to the old web site?
>> Anyone can help me to indicate me where I can find some good pages of
>> documentation, tutorial, etc. about pairwise sequence alignment for BioJava?
>>
>> Thanks a lot.
>>
>> _______________________________________________
>> Biojava-l mailing list  -  [email protected]
>> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> RCSB PDB Protein Data Bank
> Technical & Scientific Team Lead
> University of California, San Diego
>
> Editor Software Section
> PLOS Computational Biology
>
> BioJava Project Lead
> -----------------------------------------------------------------------
>

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<div dir=3D"ltr"><div><div><div><div>Hi Andreas.<br><br></div>Thank you ver=
y much for the fixes. Surely it will help me.<br></div>I have understood th=
e problem you encountered with the old site.<br></div>Now I will try to app=
ly those things.<br><br></div><div>Thanks again,<br></div><div>Andrea<br></=
div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">2016-05=
-23 19:27 GMT+02:00 Andreas Prlic <span dir=3D"ltr">&lt;<a href=3D"mailto:a=
[email protected]" target=3D"_blank">[email protected]</a>&gt;</span>:<br><blo=
ckquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #c=
cc solid;padding-left:1ex"><div dir=3D"ltr">Hi Andrea,<div><br></div><div>S=
orry for the inconvenience. We had to turn the old site off, since there we=
re too many security breaches which resulted in content spamming. This is a=
cross all bio* projects...</div><div><br></div><div>I fixed the links on th=
e CookBook4 page. Checking some of the related pages, there are still a lot=
 of formatting issues. That will take a bit to fix them all up. However, ea=
ch page at the bottom has an &quot;edit this page&quot; link, which makes i=
t easy to access the raw markdown content.=C2=A0 It is possible to see the =
code in a more readable way. I also fixed up this page for now: <a href=3D"=
http://biojava.org/wikis/BioJava:CookBook3:PSA/" target=3D"_blank">http://b=
iojava.org/wikis/BioJava:CookBook3:PSA/</a></div><div><br></div><div>Hope t=
hat helps,</div><div><br></div><div>Andreas<br><div><br></div></div><div><b=
r></div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote"><di=
v><div class=3D"h5">On Sat, May 21, 2016 at 4:09 AM, Andrea Battistelli <sp=
an dir=3D"ltr">&lt;<a href=3D"mailto:[email protected]" target=3D"_bl=
ank">[email protected]</a>&gt;</span> wrote:<br></div></div><blockquo=
te class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc so=
lid;padding-left:1ex"><div><div class=3D"h5"><div dir=3D"ltr"><div><div><di=
v><div><div><div>Hello everyone.<br><br></div>I have been studying the pair=
wise sequence alignment concept for a project that I need to do for an exam=
.<br></div><div>In particular I am interested in the global and local align=
ments and all the things related to them (how they are implemented, how I c=
an generate a paiwise alignment, ect.).<br></div>I would implement my proje=
ct in Java employing indeed BioJava as starting point.<br></div><div>I set =
up correctly the Maven project on Eclipse so no problem under that point of=
 view.<br></div><div><br></div>Few months ago I have seen there was all the=
 documentation, tutorials and specifications about the BioJava project base=
d on the Wiki pages.<br></div>I have seen it has been all migrated into a n=
ew web site but now I am not finding any documentation, tutorial or cookboo=
k about the topic of personal interest.<br><br></div>- In the BioJavaTutori=
al page - book 2, the alignment module has no pages of explanation.<br></di=
v><div>- In the CookBook4.0, all the links relative to the paiwise sequence=
 alignment give me back an &quot;<span lang=3D"en"><span>address</span> <sp=
an>uninterpretable</span></span>&quot; message.<br></div><div>- Finally in =
the Wiki Pages section there are many links. In some of these there are lin=
ks interesting for me but they contain not well formatted codes.<br><br></d=
iv><div>I know that it may taketime to migrate all the things but in the me=
antime:<br>Is there any possibility to have the reference to the old web si=
te?<br></div><div>Anyone can help me to indicate me where I can find some g=
ood pages of documentation, tutorial, etc. about pairwise sequence alignmen=
t for BioJava?<br><br></div><div>Thanks a lot.<br></div></div>
<br></div></div>_______________________________________________<br>
Biojava-l mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:[email protected]=
en-bio.org" target=3D"_blank">[email protected]</a><br>
<a href=3D"http://mailman.open-bio.org/mailman/listinfo/biojava-l" rel=3D"n=
oreferrer" target=3D"_blank">http://mailman.open-bio.org/mailman/listinfo/b=
iojava-l</a><span class=3D"HOEnZb"><font color=3D"#888888"><br></font></spa=
n></blockquote></div><span class=3D"HOEnZb"><font color=3D"#888888"><br><br=
 clear=3D"all"><div><br></div>-- <br><div><div dir=3D"ltr"><div><div dir=3D=
"ltr">---------------------------------------------------------------------=
--<br>Dr. Andreas Prlic<br>RCSB PDB Protein Data Bank</div><div>Technical &=
amp; Scientific Team Lead</div><div dir=3D"ltr">University of California, S=
an Diego<div><br></div><div>Editor Software Section=C2=A0<br><div>PLOS Comp=
utational Biology<div><div><div><br></div><div>BioJava Project Lead<br>----=
-------------------------------------------------------------------<br></di=
v></div></div></div></div></div></div></div></div>
</font></span></div>
</blockquote></div><br></div>

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