https://bsi.inscog.eu/ 2026-06-01T20:06:33+00:00 https://bsi.inscog.eu/ https://bsi.inscog.eu/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2024-11-26T15:45:46+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=emready&rev=1732635946&do=diff How to Run EMReady EMReady - Huang Laboratory Load the program : On your GPU node module load sbgrid/emready Usage: EMReady.sh in_map.mrc out_map.mrc [Options] Required arguments: * in_map.mrc: File name of input EM density map in MRC2014 format. (not the sharp map !) text/html 2024-11-26T14:17:07+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=hpc_igbmc&rev=1732630627&do=diff IGBMC HPC Cluster Storage of scientific data (link to IT page) * space2 storage (link to IT page) * mendel storage (link to IT page) Scientific calculation (link to IT page) * Quick start guide (link to IT page) * Structural biology softwares available on the cluster * AlphaFold 2 * Relion * EMReady OPEN On Demand (CryoSPARC, Rstudio server, JupyterLab) text/html 2024-08-29T07:12:25+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=relion&rev=1724915545&do=diff Relion Log in on the igbmc HPC or the team GPU ssh -X login@hpc.igbmc.fr ssh -X login@phantom-node39 #GPU node for lamour-ruff team module load relion/4.0.0 module load ctffind/4.1.13 module load topaz/0.2.5 Executable location: * CTF estimation/CTFFIND-4.1/CTFFIND-4.1 : /shared/software/ctffind/4.1.13/bin/ctffind text/html 2024-08-29T06:56:40+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=sagsub&rev=1724914600&do=diff Streptavidin affinity grids (SAG) lattice subtraction Requested files : * * * * Log onto the Lamour GPU node: ssh my_login@hpc.igbmc.fr ssh my_login@phantom-node39 Place the 4 python scripts in a SAGsub3 folder in your hpc home directory ( text/html 2024-08-07T15:51:44+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=cryosparc&rev=1723045904&do=diff using cryoSPARC modify the particles.star file from Warp The particles.star files generated by Warp during the on-the-fly processing link each particle to its tif movie. To import the particles in cryoSPARC and keep the link with the motion corrected micrographs, the star file must be edited. text/html 2024-07-25T12:08:17+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=titan_to_process&rev=1721909297&do=diff Pre-processing of dataset from Titan II 1. Recover the dataset from the microscope Log into cbi-gateway-01 to access the microscope and transfer the data to gateway or storage ssh <login>@cbi-gateway-01 ls /mnt/titan2/offloaddata/TemScripting/EF-Falcon/<dataset> rsync -avz --progress /mnt/titan2/offloaddata/TemScripting/EF-Falcon/<dataset> /mnt/storage/teams/<your_team_folder>/<project>/<dataset> text/html 2024-05-21T09:49:21+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=eer2tif_parallel.py&ns=0&rev=1716284961&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/images/fileicons/svg/py.svg" alt="eer2tif_parallel.py" loading="lazy" width="500" height="500" /> text/html 2024-05-21T09:49:21+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=eer2tif_parallel_loop.py&ns=0&rev=1716284961&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/images/fileicons/svg/py.svg" alt="eer2tif_parallel_loop.py" loading="lazy" width="500" height="500" /> text/html 2024-04-24T07:52:58+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=sagsub_3-2_stable_parallel_nils.py&ns=0&rev=1713945178&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/images/fileicons/svg/py.svg" alt="sagsub_3-2_stable_parallel_nils.py" loading="lazy" width="500" height="500" /> text/html 2024-04-24T07:52:38+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=pattern_optimizer.py&ns=0&rev=1713945158&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/images/fileicons/svg/py.svg" alt="pattern_optimizer.py" loading="lazy" width="500" height="500" /> text/html 2024-04-24T07:52:21+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=mrc_rw_3.py&ns=0&rev=1713945141&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/images/fileicons/svg/py.svg" alt="mrc_rw_3.py" loading="lazy" width="500" height="500" /> text/html 2024-04-24T07:51:53+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=gridtools.py&ns=0&rev=1713945113&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/images/fileicons/svg/py.svg" alt="gridtools.py" loading="lazy" width="500" height="500" /> text/html 2024-04-10T15:31:45+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=borate&rev=1712763105&do=diff You are a user of TBE buffer We would like to remind you that boric acid and borate have been classified as CMR (Carcinogenic, Mutagenic, Reprotoxic), in this case, toxic for reproduction. Boric acid is one of the components of the TBE (Tris Borate EDTA) buffer, widely used in molecular biology (see attached material safety data sheet). You must wear a lab coat, gloves and safety goggles when handling it. text/html 2024-04-10T15:30:07+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=h_s&rev=1712763007&do=diff Liquid chemicals and their waste Lab coat Powder chemicals to discard Ionising radiations Safety rules in the lab Boric acid, borate and TBE buffer Ethidium bromide waste Weighting CMR or T-labelled chemicals text/html 2024-03-08T16:46:24+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=e2018-cleaning_schedule_202403.png&ns=0&rev=1709916384&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=545b28&amp;media=e2018-cleaning_schedule_202403.png" alt="e2018-cleaning_schedule_202403.png" loading="lazy" width="500" height="500" /> text/html 2024-03-08T16:40:13+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=liquid-gmem.png&ns=0&rev=1709916013&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=1df2aa&amp;media=liquid-gmem.png" alt="liquid-gmem.png" loading="lazy" width="500" height="500" /> text/html 2024-03-08T16:40:13+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=gmem-vial.jpg&ns=0&rev=1709916013&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=36e518&amp;media=gmem-vial.jpg" alt="gmem-vial.jpg" loading="lazy" width="500" height="500" /> text/html 2024-03-08T16:40:13+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=gmem-bottle.jpg&ns=0&rev=1709916013&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=515af3&amp;media=gmem-bottle.jpg" alt="gmem-bottle.jpg" loading="lazy" width="500" height="500" /> text/html 2024-03-08T16:40:13+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=sodium_bicarbonate.jpg&ns=0&rev=1709916013&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=49830e&amp;media=sodium_bicarbonate.jpg" alt="sodium_bicarbonate.jpg" loading="lazy" width="500" height="500" /> text/html 2024-03-08T15:18:38+00:00 Luc Bonnefond (lbonnefond@undisclosed.example.com) https://bsi.inscog.eu/doku.php?image=e2018_media_usage.png&ns=0&rev=1709911118&tab_details=history&media_do=diff&do=media <img src="https://bsi.inscog.eu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=5c38da&amp;media=e2018_media_usage.png" alt="e2018_media_usage.png" loading="lazy" width="500" height="500" />