<div dir="ltr"><div><div><div><div>Hi Andreas.<br><br></div>Thank you very much for the fixes. Surely it will help me.<br></div>I have understood the problem you encountered with the old site.<br></div>Now I will try to apply those things.<br><br></div><div>Thanks again,<br></div><div>Andrea<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2016-05-23 19:27 GMT+02:00 Andreas Prlic <span dir="ltr"><<a href="mailto:andreas@sdsc.edu" target="_blank">andreas@sdsc.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Andrea,<div><br></div><div>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...</div><div><br></div><div>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: <a href="http://biojava.org/wikis/BioJava:CookBook3:PSA/" target="_blank">http://biojava.org/wikis/BioJava:CookBook3:PSA/</a></div><div><br></div><div>Hope that helps,</div><div><br></div><div>Andreas<br><div><br></div></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Sat, May 21, 2016 at 4:09 AM, Andrea Battistelli <span dir="ltr"><<a href="mailto:andreyas.1688@gmail.com" target="_blank">andreyas.1688@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr"><div><div><div><div><div><div>Hello everyone.<br><br></div>I have been studying the pairwise 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 alignments and all the things related to them (how they are implemented, how I can generate a paiwise alignment, ect.).<br></div>I would implement my project 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 based on the Wiki pages.<br></div>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.<br><br></div>- In the BioJavaTutorial page - book 2, the alignment module has no pages of explanation.<br></div><div>- In the CookBook4.0, all the links relative to the paiwise sequence alignment give me back an "<span lang="en"><span>address</span> <span>uninterpretable</span></span>" message.<br></div><div>- 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.<br><br></div><div>I know that it may taketime to migrate all the things but in the meantime:<br>Is there any possibility to have the reference to the old web site?<br></div><div>Anyone can help me to indicate me where I can find some good pages of documentation, tutorial, etc. about pairwise sequence alignment for BioJava?<br><br></div><div>Thanks a lot.<br></div></div>
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<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-l" rel="noreferrer" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-l</a><span class="HOEnZb"><font color="#888888"><br></font></span></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div><div dir="ltr"><div><div dir="ltr">-----------------------------------------------------------------------<br>Dr. Andreas Prlic<br>RCSB PDB Protein Data Bank</div><div>Technical & Scientific Team Lead</div><div dir="ltr">University of California, San Diego<div><br></div><div>Editor Software Section <br><div>PLOS Computational Biology<div><div><div><br></div><div>BioJava Project Lead<br>-----------------------------------------------------------------------<br></div></div></div></div></div></div></div></div></div>
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