Zhanglab forum

I am attempting to reproduce an old software tool that makes use of BioLip data. One of the requirements is that I download some old files of which the remainder of the software is based. The two files are ligand_2013-03-6.tar.bz2, and receptor_2013-03-6.tar.bz2 which were originally located at:

https://zhanggroup.org/BioLiP/download/ligand_2013-03-6.tar.bz2
https://zhanggroup.org/BioLiP/download/receptor_2013-03-6.tar.bz2

While I was able to find new versions of these files on the Biolip site, It's important I get these specific files (2013-03-6 versions). If there is anything you could do to point me to an archived version somewhere, or refer me to somewhere else I could inquire, I would appreciate the help.

The tar files you mentioned are indeed available through the links. You probably were not able to download them due to University-wide Internet outage. Please try to download them again.

Thank you, it seems like those files were a result of the outage. There is also another file that does seem to be missing. The original request I sent is to http://zhanglab.ccmb.med.umich.edu/BioLiP/download/BioLiP.tar.bz2, which resulted in a 301 (Permanently Moved) error redirecting to :

https://zhanggroup.org/BioLiP/download/BioLiP.tar.bz2

a file that does seem to actually be missing (404 Not Found). If you know where this file is, or the files that comprise the .tar file individually, I think it should solve all of my problems. I really appreciate the help.

I have uploaded that file now. Please retry download.

Thank you so much for your help! that file download seems to be working as expected now. There is one other thing that seems to have moved permanently and is no longer available for download like the previous file. For each ligand and receptor type in the weekly updates for biolip (e.g. ax) there are three files:

http://zhanglab.ccmb.med.umich.edu/BioLiP/weekly/receptor_ax.tar.bz2
http://zhanglab.ccmb.med.umich.edu/BioLiP/weekly/ligand_ax.tar.bz2
http://zhanglab.ccmb.med.umich.edu/BioLiP/weekly/BioLiP_ax.txt

Which each redirect (301 moved permanently) to the same file name at https://zhanggroup.org/BioLiP/weekly/



Two of these, the receptor and ligand files, work great and can be downloaded at :

https://zhanggroup.org/BioLiP/weekly/receptor_ax.tar.bz2
https://zhanggroup.org/BioLiP/weekly/ligand_ax.tar.bz2

The third file (BioLiP_ax.txt), however, does not seem to work. After redirecting to https://zhanggroup.org/BioLiP/weekly/BioLiP_ax.txt there is another 404 not found error. I should note that it's not just the "..._ax.txt" file I need, it's the all of the " BioLiP_[receptor_type].txt" files I need, all of which seem to be missing at that location. Please let me know if i can be more helpful in this, and thanks again for your help with my previous questions.

There is no need to download http://zhanglab.ccmb.med.umich.edu/BioL ... LiP_ax.txt
You can download all current biolip entries from https://zhanggroup.org/BioLiP/download/BioLiP.txt.gz
May I know why you need BioLiP_*.txt?

I wanted to download files in the format of http://zhanglab.ccmb.med.umich.edu/BioL ... LiP_ax.txt since these were the files queried by the software tool I'm using and attempting to recreate. If all of the information needed is in fact in:

https://zhanggroup.org/BioLiP/download/BioLiP.txt.gz

Then I would need to parse this file myself, and I cannot be sure that I'm doing it in the exact same way, with the exact same entries that the software was built on.

Dear user,
To address your request, I have uploaded all BioLiP (version 1) webserver data to
https://doi.org/10.5281/zenodo.8407896 and https://zenodo.org/record/8407920
You may concatenate the two files and decompress them by:
$ cat BioLiP1aa BioLiP1ab > BioLiP.tar.bz2
$ tar -xvf BioLiP.tar.bz2
You should be able to find whatever file you need for deprecated BioLiP file.