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  • Primary and Secondary Antibody, ICC, Blocking Good Intro: https://www.bio-rad-antibodies.com/secondary-antibody-binding-locations-benefits.htmlMatching: https://www.sigmaaldrich.com/technical-documents/articles/biology/secondary-antibody-selection.htmlHow do ...
    Posted by Danny Xu
  • Remote license server via ssh tunnel 1: what’s the hostname of your campus Mathematica license server? Something like ls01.oregonstate.edu, I’m going to call it MY_LICENSE_SERVER below. 2: what’s the ...
    Posted Aug 6, 2019, 8:48 PM by Danny Xu
  • AWS A few general and Texas-specific points:- You can buy different levels of support with different SLAs. Without paid support you are on your own.- In terms of purchasing and ...
    Posted Jul 24, 2019, 10:37 AM by Danny Xu
  • Data Backup to Box We use Google drive for the large files.  5TB max filesize, but they throttle upload speed if you exceed 750 GB in a day.  Fine for archive, but not for ...
    Posted Jul 24, 2019, 10:25 AM by Danny Xu
  • Alignment in ezCADD/NGL Open ezCADD website (http://dxulab.pharmacy.isu.edu/curry/ezCADD/main.html)Open the console of your browser. (Here is how to open it in different browser: https://kb.mailster ...
    Posted Jul 2, 2019, 3:05 PM by Danny Xu
  • Outcome server windows 10 remote desktop using rdpwrap RDPWrap on 10.0.17134.706Edit:  C:\Program Files\RDP Wrapper\rdwrap.inihttps://github.com/stascorp/rdpwrap/issues/797Hi, it worked for me. Add this to the ...
    Posted May 31, 2019, 9:13 AM by Danny Xu
  • Is it possible to use a threading adapter (e.g. M25 to RMS) and use a Nikon lens on the EVOS? The short answer is that Nikon and Olympus objectives are NOT typically compatible on the same optical system (there are a few exceptions). The key reason is that there will ...
    Posted May 15, 2019, 10:30 AM by Danny Xu
  • Confocal and Widefield Image Processing Z-Stack Step Sizehttps://www.researchgate.net/post/Whats_the_recommended_stepsize_in_a_z-stack_confocal_image_of_a_brain_slice_using_fluoview_to_better_count_cellsMicroscope ...
    Posted May 7, 2019, 8:35 PM by Danny Xu
  • EVOS LED Light Cube for DASPEI DASPEI dye (λEx/λ Em = 461/589 nm). Our EVOS FL system (AMAFD1000) contains these 4 light cubes: AMEP-4652 (RFP, Ex: 531/40 Em: 593/40)  AMEP-4650 (DAPI ...
    Posted May 7, 2019, 2:01 PM by Danny Xu
  • XAMPP  Auto installed Apache, PHP, and Perl, MySQL, can use MariaDB already installed. set up phpMyAdmin to automatically log in as user. I  also created a database user that has full ...
    Posted Feb 7, 2019, 2:24 PM by Danny Xu
  • Windows 10 in-place reinstall https://www.techspot.com/guides/1764-windows-repair-keep-all-your-files-intact/Running an in-place upgrade worked to fix our instance of Windows 10 that couldn't otherwise ...
    Posted Dec 26, 2018, 11:20 AM by Danny Xu
  • sudo preserve environment variables sudo -E su username -c 'commands'
    Posted Dec 3, 2018, 1:42 PM by Danny Xu
  • IP address lookup and block To get country and domain info from IP:geoiplookup IP_addresshost IP_address/domain_namedig whoissudo iptables -I INPUT -s x.x.x.x/32 -j DROP ...
    Posted Dec 3, 2018, 1:34 PM by Danny Xu
  • Schrodinger Installation on OpenSUSE, SUSE vi INSTALLis_sles_sled_12_sp1() {    _sles_12_sp1=`lsb_release -d 2> /dev/null | grep -e "SUSE Linux Enterprise Desktop 12\s*$" -e "SUSE Linux Enterprise Server 12 ...
    Posted Nov 17, 2018, 9:28 PM by Danny Xu
  • Mirror a website using wget and VisualWget VWget for Windows https://sites.google.com/site/visualwget/a-download-manager-gui-based-on-wget-for-windowsOptions to check:--mirror --convert-links --adjust-extension --page-requisites --no-parent --html-extension--mirror ...
    Posted Nov 8, 2018, 1:33 PM by Danny Xu
  • Hide OneDrive Sync Check Mark https://superuser.com/questions/969655/how-to-remove-onedrive-icon-overlay-checkmarks-in-windows-10
    Posted Oct 31, 2018, 6:38 PM by Danny Xu
  • GPT vs MBR Windows can only boot from GPT on UEFI-based computers running 64-bit versions of Windows 10, 8, 7, Vista, and corresponding server versions. All versions of Windows 10, 8 ...
    Posted Oct 31, 2018, 9:47 AM by Danny Xu
  • libstdc++.so.5 error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directorySolution: search for "libstdc" in yast2, most likely libstdc++33-32bit package ...
    Posted Oct 23, 2018, 10:05 AM by Danny Xu
  • Windows 10 update "your virus and threat protection is managed by your organization" https://www.reddit.com/r/Windows10/comments/8rn6wb/your_virus_threat_protection_is_managed_by_your/https://www.windowsdigital.com/your-virus-and-threat-protection-is-managed-by-your-organization ...
    Posted Jul 29, 2019, 1:02 PM by Danny Xu
  • Pin a folder to Task bar from Windows File Explorer https://social.technet.microsoft.com/Forums/windows/en-US/ac50ecfb-cc7f-4991-8bcf-bafe5404f665/how-to-pin-a-folder-to-the-pinned-file-explorer-pinned-list?forum=w8itprogeneralDrag and ...
    Posted Oct 31, 2018, 9:56 AM by Danny Xu
  • Adobe Acrobat OCR text recognition renderable text error https://helpx.adobe.com/acrobat/kb/error-could-perform-recognition-acrobat.html Issue When you start the Recognize Text Using OCR command, Adobe Acrobat returns the following error:"Acrobat could ...
    Posted Oct 20, 2018, 5:06 PM by Danny Xu
  • Windows Log file for Crash, etc. https://www.digitalmastersmag.com/magazine/tip-of-the-day-how-to-find-crash-logs-on-windows-10/
    Posted Oct 11, 2018, 2:58 PM by Danny Xu
  • PSCI 6670 CADD I For oddt environment, installed oddt,  openbabel 2.4.0 from oddt channel, rdkit/chemfp from bioconda channel For rotatable bonds in Openbabel, I need to modify plugindefine.txt in this ...
    Posted Oct 1, 2018, 1:21 PM by Danny Xu
  • Create LVM over RAID0 https://wiki.archlinux.org/index.php/Software_RAID_and_LVM This section will convert the two RAIDs into physical volumes (PVs). Then combine those PVs into a volume group (VG ...
    Posted Sep 25, 2018, 12:27 PM by Danny Xu
  • Dell T5500 Opensuse 42.3 Installation Kernel Parameter Need to tweak ACPI setting to install 42.3 https://tr.opensuse.org/SDB:Kernel_Parameters_for_ACPI/APICBefore installation, need to set acpi=offAfter installation, remove acpi ...
    Posted Aug 28, 2018, 4:16 PM by Danny Xu
  • Linux strings command Process text in a binary filehttps://fossbytes.com/strings-command-linux-tool/strings `which cat` | grep license
    Posted Aug 27, 2018, 9:39 AM by Danny Xu
  • SSD NVME M2 Speed Performance Test For Micron/Crucial SSD, There is Momentum Cache  option. Download and install Storage Executive option.https://www.crucial.com/wcsstore/CrucialSAS/pdf/enhancing_performance_momentum_cache.pdfFor Samsung regular ...
    Posted Oct 12, 2018, 1:50 PM by Danny Xu
  • SAS and Python, SASPy, SAS_Kernel for Jupyter Notebook SAS Programming for R Users (Course Materials)https://github.com/sassoftware/sas-prog-for-r-usersIn SAS environments outside of SAS University Edition, here's what you need to ...
    Posted Mar 27, 2018, 6:23 PM by Danny Xu
  • Log compilation, installation steps ./configure --prefix=/home/you/mpich-install  2>&1 | tee config.log  (bash)|& tee (csh)make VERBOSE=1 |& tee make.log (for csh and tcsh) make VERBOSE=1 2>&1 | tee ...
    Posted Feb 15, 2018, 9:27 AM by Danny Xu
  • Linux hardware info sudo /usr/sbin/dmidecodFor details:http://www.tricksguide.com/get-hp-hardware-information-using-dmidecode-command-in-linux.html
    Posted Feb 14, 2018, 2:45 PM by Danny Xu
  • M.2 drive SSD vs NVMe Are all M.2 drives NVMe? No. Remember, M.2 is just the form factor. M.2 drives can come in SATA versions (like the Crucial MX300 M.2 for ...
    Posted Feb 7, 2018, 11:13 AM by Danny Xu
  • View and convert SVG file on Linux and Windows On SUSE, install rsvg-view from yast2Viewer:  rsvg-view-3 filename.svgConverter:  -f, --format=[png, pdf, ps, eps, svg, xml, recording] rsvg-convert C2-C1-C3-C6.svg ...
    Posted Feb 6, 2018, 10:58 AM by Danny Xu
  • Sqlite vs MySQL http://www.sqlite.org/whentouse.htmlhttps://stackoverflow.com/questions/4813890/sqlite-or-mysql-how-to-decide
    Posted Jan 14, 2018, 5:21 PM by Danny Xu
  • tar to stdout tar xvf archive.tar -O | lesstar xvf archive.tar -O | grep [ ]For a file inside tar filetar xvf archive.tar file_with_path -O | lesstar xvf archive ...
    Posted Jan 10, 2018, 9:07 PM by Danny Xu
  • CXX11 compilation error https://gcc.gnu.org/onlinedocs/libstdc++/manual/using_dual_abi.html If you get linker errors about undefined references to symbols that involve types in the std::__cxx11 namespace or ...
    Posted Jan 6, 2018, 10:00 AM by Danny Xu
  • Amber16 + AmberTool17 installation sudo conda create -n amber16 python=2.7install the following packages:numpymatplotlibscipyipythonnotebookcythonsudo yast2install  libbz2-1 libbz2-develexport AMBERHOME=/garlic/apps/Downloads ...
    Posted Feb 15, 2018, 3:46 PM by Danny Xu
  • MDL Mol/SDF V2000 vs V3000 Most apps: obabel, ChemAxon etc. can handle the conversion:http://open-babel.readthedocs.io/en/latest/FileFormats/MDL_MOL_format.htmlhttps://forum.chemaxon.com/ftopic10939.htmlhttp://wiki.jmol ...
    Posted Dec 24, 2017, 3:31 PM by Danny Xu
  • CMake find OpenBabel installed in Conda The magic line is in cmake/modules/FindOpenBabel2.cmake                NAMES                        openbabel/obconversion.h                        openbabel-2.0/openbabel/obconversion.h
    Posted Dec 21, 2017, 1:17 PM by Danny Xu
  • Install gnina and Caffe https://github.com/gnina/gninagit clone https://github.com/gnina/gnina.git cd gninaTip: vi CMakeCache.txt to debugCreate conda env gnina with python2.7 and install ...
    Posted Jan 5, 2018, 8:09 PM by Danny Xu
  • Minerve2 Backup Procedure 1. login to minerve2 and package all files in your home folder to a tar filenohup tar cvpf minerve2_backup.tar . >& minerve2_backup.log &tail -f minerve2_backup.log ...
    Posted Dec 4, 2017, 4:48 PM by Danny Xu
  • LVM commands on an external eSata/USB3 enclosure Volume Group commands vgscan Scans all the disks for volume groups and rebuilds the LVM cache file, also displays the volume groups. vgchange -a n/y my_volume_group Deactivate ...
    Posted Dec 4, 2017, 2:53 PM by Danny Xu
  • Auto delete Gmail Step 1: Go to Settings -> Filters -> Create a new filter Step 2: Type the following into "Has the words" field: category:promotions older_than:90dor before:2011/01/15 ...
    Posted Dec 3, 2017, 9:16 AM by Danny Xu
  • MongoDB and LINCS L1000 1. Open Robot 3T and click create 2. Fill out connection as shown then hit Authentication tab 3. Check Perform authentication and fill out the fields. The password is dxu123 ...
    Posted Nov 28, 2017, 5:59 PM by Danny Xu
  • Map any key to any key on Windows https://superuser.com/questions/36920/how-can-i-remap-a-keyboard-keyhttps://github.com/randyrants/sharpkeys/releases
    Posted Nov 18, 2017, 10:17 AM by Danny Xu
  • Ginger iptables outbound rules -A OUTPUT -m state --state RELATED,ESTABLISHED -j ACCEPT-A OUTPUT -p tcp -m tcp --dport 22 -j ACCEPT-A OUTPUT -p tcp -m tcp --dport 53 -j ACCEPT-A ...
    Posted Nov 6, 2017, 12:39 PM by Danny Xu
  • Add a Domain name to Google Site Follow instructions here https://www.namesilo.com/Support/Google-Verification-and-Blogger-InstructionsStep 1 Make sure your domain is using our default name servers. Your domain must be using ...
    Posted Nov 4, 2017, 10:17 AM by Danny Xu
  • Cat concatenate gz files https://www.biostars.org/p/81924/cat file1.gz file2.gz file3.gz > allfiles-cat.gz zcat file1.gz file2.gz file3.gz | gzip -c > allfiles-zcat.gz zcat allfiles ...
    Posted Oct 26, 2017, 1:30 PM by Danny Xu
  • Windows Subsystem for Linux (WSL), Anaconda, Conda, Jupyter Wow!!! Starting in Windows 10 Anniversary Update, the Windows Subsystem for Linux can invoke native Windows binaries from the Linux console and Linux binaries from a Windows console.  https://msdn ...
    Posted Jan 29, 2019, 8:32 PM by Danny Xu
  • Convert SVG to PNG or JPG https://stackoverflow.com/questions/9853325/how-to-convert-a-svg-to-a-png-with-image-magick  I haven't been able to get good results from ImageMagick in this instance ...
    Posted Oct 24, 2017, 10:26 AM by Danny Xu
  • SCM-ADF https://www.scm.com/doc/Installation/Linux_Quickstart_Guide.htmlADF2017 uses VTK7 and newer OpenGL features to dramatically speed up the visualization of large systems. This comes with a ...
    Posted Apr 26, 2017, 2:09 PM by Danny Xu
  • Encrypt shell script on Linux and BAT file on Windows Linux ShellHow to: http://www.thegeekstuff.com/2012/05/encrypt-bash-shell-script/?utm_source=tuicoolDownload shc: http://www.datsi.fi.upm.es/~frosal/shc -r -f ./script ...
    Posted Oct 17, 2017, 2:39 PM by Danny Xu
  • Rdkit Cairo Fix for Drawing Molecules from rdkit import Chemfrom rdkit.Chem import AllChemfrom rdkit.Chem import DrawAllChem.Compute2DCoords(m)m = Chem.MolFromSmiles('c1nccc2n1ccc2')Draw.MolToFile(m,'/tmp/test.png')Errors pops up ...
    Posted Apr 18, 2017, 5:00 PM by Danny Xu
  • Linux Cheat Sheet
    Posted Apr 11, 2017, 5:30 PM by Danny Xu
  • Anaconda conda https://stackoverflow.com/questions/34441943/ipython-installed-but-not-foundipython in Schrodinger virtual env http://content.schrodinger.com/Docs/r2016-2/python_api/intro.htmlalias ipython='python -m ...
    Posted Sep 18, 2017, 12:46 PM by Danny Xu
  • APC Smart UPS The packages are: apcupsd and apcupsd-gui The status of the daemon can be found with: systemctl status apcupsd.service The graphical interface is: gapcmon And the config file is ...
    Posted Feb 23, 2017, 3:34 PM by Danny Xu
  • Ginger iptables/firewall It's turned on. To change config: vi /etc/iptables/rules.v4
    Posted Jan 30, 2017, 6:34 PM by Danny Xu
  • netcat/nc port scan https://www.cyberciti.biz/faq/linux-port-scanning/Check if a port is opennc -z -v -w5 <host> <port/range>-w5: 5s timeout is optionalExample: nc -zv domain ...
    Posted Nov 2, 2017, 1:20 PM by Danny Xu
  • Firefox 48 update on SLES 12 SP1 Initial update caused breaking of default Gnome Login Screen, the following will prevent it: 1. Open Yast2-->Software-->Software Management 2. Search for firefox 3. Select MozillaFirefox and bring up ...
    Posted Dec 15, 2016, 3:06 PM by Danny Xu
  • awk over ssh runhost.sh all "ps aux|grep virtualgrid|awk '{print \$2}'|head -1|xargs -ti kill {}"runhost.sh all 'nohup virtualgrid -nogui >& virtualgrid_`hostname`.log&'
    Posted Oct 14, 2016, 4:11 PM by Danny Xu
  • Real CPU Load top -b -n2 -p 1 | fgrep "Cpu(s)" | tail -1 | awk -F'id,' -v prefix="$prefix" '{ split($1, vs, ","); v=vs[length(vs)]; sub("%", "", v); printf "%s%.1f%%\n", prefix ...
    Posted Oct 1, 2016, 8:23 PM by Danny Xu
  • Check python unicode version ucs2 vs ucs4 This is for python 2.7When built with --enable-unicode=ucs4: >>> import sys >>> print sys.maxunicode 1114111 When built with --enable-unicode=ucs2: >>> import sys >>> print sys.maxunicode 65535 ...
    Posted Feb 23, 2017, 10:04 AM by Danny Xu
  • Remove python apps installed through “python setup.py install” "You need to remove all files manually, and also undo any other stuff that installation did manually. If you don't know the list of all files, you can reinstall ...
    Posted Sep 6, 2016, 11:59 PM by Danny Xu
  • Anaconda env for multi-users https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/qinxkmvlnSg sudo su - adduser anaconda mkdir /opt/anaconda ./path/to/Anaconda-latest.sh -b -p /opt/anaconda chown -R anaconda ...
    Posted Sep 6, 2016, 10:03 PM by Danny Xu
  • Monitor Installer/Program Changes in Windows 8 suggested tools https://www.raymond.cc/blog/tracking-registry-and-files-changes-when-installing-software-in-windows/Microsoft suggested tools https://msdn.microsoft.com/en-us/library/dd873573.aspx ...
    Posted Aug 26, 2016, 12:00 PM by Danny Xu
  • SUSE12 clone OS Disk Grub2 ext4 1. Use ddrescue to close to a new disk via USB3. Note that the source OS drive does not need umount2. The new disk should be able to boot ...
    Posted Aug 23, 2016, 5:38 PM by Danny Xu
  • GPU Overclock http://www.acceleware.com/blog/gpu-boost-nvidias-tesla-k40-gpushttp://cryptomining-blog.com/7341-how-to-squeeze-some-extra-performance-mining-ethereum-on-nvidia/https://devblogs.nvidia.com ...
    Posted Aug 17, 2016, 4:13 PM by Danny Xu
  • GPU fan speed control 1. Do this only onceEnabling Control of Fan Speed and generate xorg.conf file, Adds coolbits to the xorg filesudo nvidia-xconfig -a --cool-bits=28 --allow-empty ...
    Posted Aug 30, 2016, 3:57 PM by Danny Xu
  • Windows 8 AppLocker https://www.youtube.com/watch?v=ab5IGQr70-ghttps://www.youtube.com/watch?v=HAts_oDDdfQhttps://www.youtube.com/watch?v=Msbh56Iirbkhttps://www.youtube.com/watch?v=Z2 ...
    Posted Aug 12, 2016, 5:42 PM by Danny Xu
  • Windows 8 NSF http://superuser.com/questions/525473/how-do-i-mount-an-nfs-share-in-windows-8No NFSv4 Support!! only NFSv3 supportFor v4 support, try UMich program http://www.citi ...
    Posted Aug 12, 2016, 5:48 PM by Danny Xu
  • Windows 8 and 10 Remote Desktop RDP Hack Windows 10https://appuals.com/how-to-setup-rdp-on-windows-10-all-versions/https://github.com/stascorp/rdpwrap/releaseshttps://www.serverwatch.com/server-tutorials/remote-desktop-connections-for ...
    Posted Feb 12, 2019, 10:55 AM by Danny Xu
  • NVRM: os_schedule: Attempted to yield the CPU while in atomic or interrupt context This is GPU0 Titan Z in peppersee https://forums.gentoo.org/viewtopic-p-7588226.html[   26.328777] nvidia-modeset: Loading NVIDIA Kernel Mode Setting Driver for UNIX platforms  361 ...
    Posted Aug 14, 2016, 8:35 AM by Danny Xu
  • File encryption using OpenSSL and PGP Tar the directory tar cvf backup.tar /path/to/folder You can remove the [v] switch from the tar command to switch off the verbose mode. Encrypt openssl aes-256 ...
    Posted Aug 3, 2016, 10:29 AM by Danny Xu
  • Startup scipt for ubuntu 1. simple, requires rootvi /etc/rc.local2. upstart systemA simple command (one which doesn't need to remain running) could use an Upstart job like: start on ...
    Posted Aug 2, 2016, 5:18 PM by Danny Xu
  • Bash commands usage examples: sed, awk etc. #awk one linerhttp://www.pement.org/awk/awk1line.txthttp://tuxgraphics.org/~guido/scripts/awk-one-liner.html#sed one-linerhttp://sed.sourceforge.net/sed1line.txthttp://www ...
    Posted Oct 8, 2016, 11:10 PM by Danny Xu
  • Well said about GPUs, applicable to computing http://furryball.aaa-studio.eu/aboutFurryBall/benchmarks.html Always use the latest NVIDIA drivers! (some older versions can cause crashing of FurryBall) Remember, if you will use FurryBall with OLD ...
    Posted Aug 2, 2016, 5:20 PM by Danny Xu
  • BUG: soft lockup - CPU#1 stuck for 22s! [Xorg:2982] Solution: disabling C-states in the BIOS  and other CPU power-saving options such as Turbo Mode/Turbo Boost  etc.. should fix this.Some people also tried adding clocksource=jiffies ...
    Posted Feb 19, 2018, 9:30 AM by Danny Xu
  • Remove an IP address that DenyHosts blocked? /etc/denyhosts.confWORK_DIR=/var/lib/denyhostsIf you have been accidentally locked out of one of your hosts (because DenyHosts has added it to /etc/hosts.deny you ...
    Posted Apr 25, 2017, 3:34 PM by Danny Xu
  • Check Linux distro version, LSB, and diagnose binary file Count number of CPUsgrep -c ^processor /proc/cpuinfo mpstat -P ALL|head -1|cut -d'(' -f3|cut -d')' -f1Distro version (this will also show LSB version): lsb_release ...
    Posted Aug 2, 2016, 4:50 PM by Danny Xu
  • MAC address Start/stop network interfaceOld SUSEhttp://www.cyberciti.biz/faq/novell-sles-suse-restart-stop-networking-services-networking/SUSE11 ifup, ifdown, ifstatus https://www.suse.com/documentation/sled11/book ...
    Posted Jul 26, 2016, 1:09 AM by Danny Xu
  • Basename ${variable%pattern} Trim the shortest match from the end ${variable##pattern} Trim the longest match from the beginning ${variable%%pattern} Trim the longest match from the end ${variable#pattern} Trim ...
    Posted Jul 22, 2016, 8:23 PM by Danny Xu
  • Passwordless for sudo over ssh 1) sudo vi /etc/sudoers: jenkins ALL=(ALL) NOPASSWD: ALL 2) Put the line after all other lines in the sudoers file! That worked for Ubuntu 14.4 and SUSE12 ...
    Posted Jul 21, 2016, 12:10 AM by Danny Xu
  • Configure sshd openssh https://en.opensuse.org/SDB:Configure_openSSHWhenever you made a change to /etc/ssh/sshd_config you must restart the SSHD or make it reload its configuration by typing ...
    Posted Jul 21, 2016, 12:04 AM by Danny Xu
  • After.local You can also write your scripts and then execute them from /etc/init.d/after.local and /etc/init.d/halt.local The after.local script will be run after ...
    Posted Jul 20, 2016, 7:16 PM by Danny Xu
  • IPTables persistent https://blog.remibergsma.com/2013/02/12/automating-persistent-iptables-rules-on-red-hat-suse-and-debian/https://www.digitalocean.com/community/tutorials/how-to-implement-a-basic-firewall-template ...
    Posted Jul 20, 2016, 6:57 PM by Danny Xu
  • Schrodinger Docs Maestro-11 Reference Cardhttps://www.schrodinger.com/sites/default/files/maestro_11_qrc.pdf2018-1https://www.schrodinger.com/sites/default/files/s3/mkt/Documentation/2018-1/docs ...
    Posted May 28, 2018, 5:15 PM by Danny Xu
  • clusterssh/cssh - multiple host ssh/exec https://github.com/duncs/clusterssh/wikiNeed to install tk.pm package for perlas root cpan -i Tk
    Posted Jul 14, 2016, 4:54 PM by Danny Xu
  • GPU nvidia-smi and Schrodinger Schrodinger:Second, ensure that all your cards have ECC memory turned off, are set to Exclusive Process Mode, and Persistence Mode is on. Disable ECC by running the following command ...
    Posted Aug 11, 2016, 10:10 PM by Danny Xu
  • Disable VMD GPU use You must set the CUDA-related environment variables in your shell prior to launching VMD. In the case of Unix systems, you'd do this: /bin/csh syntax: setenv VMDNOCUDA ...
    Posted Jul 15, 2016, 1:13 PM by Danny Xu
  • IPTables Block IP and IP Range This is the correct way: iptables -A INPUT -p tcp --match multiport --dport 1024:3000 -j ACCEPT As an example. Source here. iptables -A INPUT -p tcp --dport 1000:2000 ...
    Posted Jul 12, 2016, 7:57 AM by Danny Xu
  • SUSE12 Desktop Login Problems 1. If login windows does not show up, press CTRL-ALT-Backspace2. If still doesn't work, login as root, init 3init 5rm /run/nologinOtherwise "System ...
    Posted Jul 11, 2016, 3:34 PM by Danny Xu
  • Fail2ban unban IP   With Fail2Ban before v0.8.8: fail2ban-client get YOURJAILNAMEHERE actionunban IPADDRESSHERE With Fail2Ban v0.8.8 and later: fail2ban-client set YOURJAILNAMEHERE unbanip IPADDRESSHERE The hard part is finding ...
    Posted Jul 12, 2016, 7:46 AM by Danny Xu
  • Xargs ~$ echo 10 20 30 40 50 60 | xargs -n 1 -P 4 sleep The use of “-n 1” is vital if you want to pass only one command-line argument ...
    Posted Jul 9, 2016, 10:12 AM by Danny Xu
  • Super fast backup. copy, move many files To copy a large amount of data, tar is generally faster than rsync. The idea is to start with tar and finish off with a final rsync,tar -cpf - src ...
    Posted Jul 6, 2016, 11:09 PM by Danny Xu
  • Find examples 1. Recursively delete empty directories The find command is the primary tool for recursive, filesystem operations. Use the -type d expression to tell find you're interested in finding directories ...
    Posted Jul 5, 2016, 6:58 PM by Danny Xu
  • Super fast delete a folder with large number of files http://www.slashroot.in/which-is-the-fastest-method-to-delete-files-in-linuxtime perl -e 'for(<*>){((stat)[9]<(unlink))}'time find ./ -type f -delete (the BEST)time rsync ...
    Posted Jul 6, 2016, 9:20 AM by Danny Xu
  • Memory editing read: http://eryanbot.com/jtp/2012/06/26/game-hacking-basics-memory-editing-linux/http://ftlwiki.com/wiki/Cheats#Memory_Editing_on_LinuxLinux: scanmem https://github.com/scanmem/scanmem ...
    Posted Aug 2, 2016, 3:45 PM by Danny Xu
  • White Label hard drives For Windows, use freeware http://hddscan.com/Stress test https://www.jam-software.com/heavyload/https://forums.servethehome.com/index.php?threads/review-of-white-label-4tb-drives.3559/Testing ...
    Posted Oct 12, 2018, 5:17 PM by Danny Xu
  • GPU stress test gpu_burn-0.6.tar.gz (compatible with nvidia-smi and nvcc as of 04-12-2015)This is the best GPU test along with megadock.Note: must run the ...
    Posted Aug 9, 2016, 10:52 AM by Danny Xu
  • SUSE Rescue mode and chroot 1. Start the system with the rescue CD 2. Login with root (no password needed) 3. Mount the / partition. mount /dev/sdc3 /mntmount /dev/sdc1 /mnt/boot4. Give ...
    Posted May 23, 2016, 6:51 PM by Danny Xu
  • How to search DTP/NCI Compounds An easier option is to use Enhanced NCI Database Browser 2.2https://cactus.nci.nih.gov/ncidb2.2/In Query Data Value, paste SMILES string and set Tc threshold ...
    Posted Sep 5, 2016, 2:34 PM by Danny Xu
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Primary and Secondary Antibody, ICC, Blocking

posted Aug 18, 2019, 12:51 PM by Danny Xu   [ updated ]




  1. How do I decipher the secondary antibody nomenclature?
    Anti-Goat IgG (H+L), highly cross-adsorbed, CF™ 568 antibody produced in donkey

Immunoglobulin Ig Classes and Isotypes

There are five mammalian immunoglobulin (Ig) classes where the heavy chain differs in amino acid composition and number: IgA (alpha), IgD (delta), IgE (epsilon), IgG (gamma) and IgM (mu). As there are five different Ig antibody classes, it can be advantageous to select a secondary raised against a specific class. Immunoglobulin classes, subclasses and their binding valency are described fully here.

The table below shows the different Ig classes and subclasses/isotypes in human and mouse.

Ig Class 

Human Ig Subclasses

Mouse Ig Subclasses

IgA

IgA1

IgG1

IgD

IgA2

IgG2a

IgE

IgG1

IgG2b

IgG

IgG2

IgG3

IgM

IgG3

 

 

IgG4

 

IgG Antibody

IgG Antibody IgG Structure

  • Two heavy chains: each chain composed of VH, CH1, hinge region, CH2 and CH3
  • Two light chains: each chain composed of VL and CL. There are two types of light chain, called kappa and lambda, always identical for each antibody
  • Two antigen binding sites: found at the end of the VH and VL chain, known as the paratope
Key  

Fv = Fragment, variable region

Fc = Fragment, crystallisable region

VH = Variable heavy chain

VL = Variable light chain

CH1 = Constant heavy chain 1

CL = Constant light chain

CH2 = Constant heavy chain 2

CH3 = Constant heavy chain 3

Fab = Fragment, antigen binding region

Fd = Heavy chain of the Fab

Lc = Light chain of the Fab

 

Click here for further information on IgG and the antibodies available to this Ig class.

Back to top

IgA Antibody

IgA Antibody IgA Structure

  • Four alpha heavy chains
  • Four light chains
  • Tetravalent
  • One secretory protein chain
  • One joining (J) chain

 

 

Click here for further information on IgA and the antibodies available to this Ig class.

IgD Antibody

IgD Antibody IgD Structure

  • Two delta heavy chains
  • Two light chains
  • Bivalent
  • Does not bind to Fc receptors

 

 

 

Click here for further information on IgD and the antibodies available to this Ig class.

IgE Antibody

IgE Antibody IgE Structure

  • Two epsilon heavy chains
  • Two light chains
  • Bivalent
  • Heavy chains contain a unique CH4 domain not found in other classes

 


 

Click here for further information on IgE and the antibodies available to this Ig class.

IgM Antibody

IgM Antibody IgM Structure

  • Pentamer of bivalent subunits
  • Ten Mu heavy chains
  • Ten light chains
  • One Joining (J) chain
  • Decavalent
  • Considerably higher molecular mass than other classes
     

 

Click here for further information on IgM and the antibodies available to this Ig class.


In what species was the primary antibody developed?
Secondary antibodies are directed against the species of the primary antibody. Therefore, you will need a secondary antibody that is raised in a species different than the host species of the primary antibody. For example if your primary antibody is raised in a mouse, you will need an anti-mouse secondary antibody raised in goat, rabbit, etc.

What is the class (isotype) and/or subclass of the primary antibody?
This question is primarily important when working with monoclonal antibodies. Polyclonal antibodies, however, are typically IgG class immunoglobulins. For this reason, the secondary antibodies will mainly be an anti-IgG antibody.

Monoclonal antibodies are most commonly developed in mice and occasionally in rats, hamsters or rabbits. For example, if the primary monoclonal antibody is mouse IgM, one would want a secondary antibody that reacts with mouse IgM (anti-Mouse IgM).

If the primary monoclonal is one of the mouse IgG subclasses, almost any anti-mouse IgG secondary antibody should bind to it. If the subclass of the primary antibody is not known, then anti-Mouse IgG F(ab) secondary antibodies may be used since they recognize most mouse immunoglobulin subclasses.

Primary ABs:
Mark W. Recommended HCS-1 is mouse Monoclonal IgG2a, http://dshb.biology.uiowa.edu/hcs-1 

Storage and Handling Recommendations: Although many cell products are maintained at 4°C for years without loss of activity, shelf-life at 4°C is highly variable. To ensure retention of antibody activity, we recommend aliquotting the product into two parts: 1) a volume of antibody stored at 4°C to be used within two weeks. 2) the remaining product diluted with an equal volume of molecular grade glycerol and stored at -20°C.

P.W.: Anti-Parvalbumin Millipore Sigma MAB1572 is Mouse Monoclonal  IgG1   Storage and Stability  Stable for 1 year at -20ºC from date of receipt.
mainly use the mouse monoclonal from Millipore Sigma (MAB1572). The one in rabbit would work as well. Apparently the trick is to block with goat serum when staining zebrafish; other serums do not work as well.  We usually order our secondaries from Molecular Probes through Thermo Fisher, although we're trying out a new source that's slightly cheaper, Jackson Immunoresearch.


Secondary Abs: Alexa Fluor® 488 AffiniPure Goat Anti-Mouse IgG (H+L) https://www.jacksonimmuno.com/catalog/products/115-545-003

Physical State: Freeze-dried solid 
Storage and Rehydration: Store freeze-dried solid at 2-8°C. Rehydrate with the indicated volume of dH2O and centrifuge if not clear. Prepare working dilution on day of use. Product is stable for about 6 weeks at 2-8°C as an undiluted liquid.
Extended Storage after Rehydration: Aliquot and freeze at -70°C or below. Avoid repeated freezing and thawing.

Alternatively, add an equal volume of glycerol (ACS grade or better) for a final concentration of 50%, and store at -20°C as a liquid.

Expiration date: one year from date of rehydration. The expiration date may be extended if test results are acceptable for the intended us


There are many classes and subclasses of human and mouse IgG(s). Choosing a secondary may be difficult. However, one common factor among these IgG(s) are the light chains (kappa and lambda). In other words, IgG, IgM, IgA, IgD and IgE all have either kappa or lambda light chains. The heavy chain, however, is class specific.

Summary of immunoglobulin classes and subclasses:
         Immunglobulin Classes: IgG, IgM, IgA, IgE, IgD
         Human Immunoglobulin Subclasses: IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2
         Mouse Immunoglobulin Subclasses: IgG1, IgG2a, IgG2b, IgG3
         Light Chains: Kappa, Lambda
         Heavy Chains: IgG (gamma), IgM (mu), IgA (alpha), IgD (delta), IgE (epsilon)


Additional information on antibody reactivities:
  • Polyvalent: react with all classes
  • Anti-Fc and heavy-chain specific: react with heavy chains only, therefore, they are class specific.
  • Anti-Fab and whole molecule specific: react with heavy and light chains. Due to the light chain reactivity, they can react with all classes.
  • Light chain (kappa, lambda) specific: react with all classes, since all classes use the same kappa or lambda light chains.

Secondary Antibody Specific Binding Locations

The nature of the epitope recognized by the secondary antibody can have an impact on the success of an experiment, and it is worth taking the time to consider if this may affect your data. Here we have divided our secondary antibody range into four groups based on the epitope recognized.

1. Universal

H/L chain – these polyclonal secondary antibodies have a broad target binding area as they recognize both the heavy and light chains, which are found in all formats (full Ig, F(ab)2’ and Fab’) and classes of primary antibodies.
 

Example of use - due to their broad reactivity, universal polyclonal secondary antibodies can be used in most applications when specificity is not an issue. See the example of western blotting in the following section:  “Detection of light and heavy chains of a mouse monoclonal IgG1 by western blot analysis”. 

2. Light chain

Ig lambda light chain or kappa light chain – light chain specific secondary antibodies will target 25 kDa polypeptides without detecting the heavy chain. Light chain ratios vary greatly between species, and secondary antibodies are not generally cross-reactive, so it is important to establish the specific light chain in your primary antibody when using this type of secondaries.

Example of use - western blotting of immunoprecipitates may cause detection problems if the antigen is of a similar size to the 50 kDa heavy chain of IgG, this is because the secondary may detect this component of the precipitating primary antibody. The use of an anti-light chain secondary antibody will prevent this, as only the 25 kDa light chain will be co-detected in the blot. See an example blot in the following section: “Detection of light and heavy chains of a mouse monoclonal IgG1 by western blot analysis”. 

3. Heavy chain

  1. Gamma chain – these secondary antibodies target the heavy chain found in full IgG, F(ab)2’ and Fab’ formats. They do not cross-react with IgG light chains.
  2. Mu chain – these secondary antibodies only recognize the heavy chain on IgM, and as a result, no cross-reactivity is seen with other Ig class heavy chains or any Ig light chains.
  3. Alpha chain and alpha 1 chain – these secondary antibodies recognize the alpha chain on IgA subclass, and have minimal cross-reactivity with other human immunoglobulin subclasses.
  4. Fc – these secondary antibodies recognize the Fc region of a specific and specified Ig subclass. They can be useful to capture primary antibodies with their antigen binding domains clearly presented.
  5. CH2 domain (CH3 in IgM and IgE) – these secondary antibodies recognize the CH2 domain on the heavy chain in the Fc region of a specific and specified Ig subclass. The CH2 domain in an antibody has a role in preventing degradation in vivo, and may be added to therapeutic proteins to increase their half-life. Read secondary antibodies to CH2 and CH3 domains for further information about how secondary antibodies specifically targeted to the CH2 and CH3 domains of immunoglobulins enable the study of the Fc fragments in the development of new therapeutic antibody fragments.
  6. CH3 domain – these secondary antibodies recognize the CH3 domain on the heavy chain in the Fc region of a specific and specified Ig subclass. As above, this region plays a role in antibody stability.
  7. Hinge region – these secondary antibodies recognize the hinge region of a specific and specified Ig subclass.
  8. Fd – these secondary antibodies recognize the Fd region of human IgG. The Fd region is the heavy chain of the Fab, i.e. approximately the first 220 amino acids from the N-terminus of the heavy chain comprised of the VH and CH1 regions.  Typically these antibodies show minimal cross-reactivity to the Fc region of human IgG and other human immunoglobulins.
     

Example of use - in an analogous situation to the one described above, the use of an anti-heavy chain secondary can prevent interference with the detection of antigens of a similar size to the 25k Da IgG light chain of the precipitating primary antibody by only detecting the larger heavy chain component. See example western blot data in the following section: “Detection of light and heavy chains of a mouse monoclonal IgG1 by western blot analysis”. 



When should I use a pre-adsorbed secondary antibody?
Using pre-adsorbed antibodies will reduce non-specific background when working with tissues and cells. The process involves passing the secondary antibody over immobilized serum proteins from potentially cross reactive species. Therefore, if you are working with human tissues, choose a secondary antibody that has been adsorbed with human serum or human IgG.

Cross-Adsorbed Antibodies
  1. Cross reactions are often seen with secondary antibodies. For example, anti-mouse IgG may cross react to some degree with rat IgG, or an anti-rat IgG may show some cross reaction with IgM, and an anti-mouse IgG2a may show some cross reaction with mouse IgG2b. In some cases cross reactivity is not significant, but in others a high degree of specificity is required for accurate data.

    The initial way to achieve specificity is to use a cross-adsorbed polyclonal secondary. Here unwanted cross-reactivity is removed by pre-adsorption of the secondary antibody with the cross reacting antigen, to yield a more specific secondary and therefore reduce non-specific background staining. As an alternative to this, a monoclonal secondary may be selected that binds to an epitope unique to the chosen isotype.

    Read our overview on cross-adsorbed secondary antibodies to discover why and how you should use them, how they are generated, and a list of the cross-adsorbed secondary antibodies available now.



  2. When is a F(ab) or F(ab')2 fragment antibody necessary?
    If working with tissues or cells that have Fc receptors, choose a F(ab) or F(ab')2 fragment when possible to eliminate non-specific binding.  In more detail, F(ab')2 antibody fragments are used in assay systems where the presence of the Fc region may cause problems. Samples such as lymph nodes, spleen, and peripheral blood preparations contain cells with Fc receptors (macrophages, B lymphocytes, and natural killer cells) which could bind the Fc region of intact antibodies, causing high background staining. Use of F(ab')2 fragments ensures that any antibody binding observed is not due to Fc receptors.
Andy Groves Lecture@BIE 2019




Blocking Explained


Preventing Non-specific Staining

Once tissue or cell samples have been appropriately prepared and fixed, the samples are ready to be stained. All IHC/ICC studies are dependent on specific antibody-epitope binding, which is governed by hydrophobic interactions, ionic interactions, hydrogen bonding, and other intermolecular forces. However, the same attractive forces can also result in non-specific staining, i.e. binding of the primary antibody to amino acids other than those within the desired epitope of the antigen. This is a common problem that occurs in IHC/ICC experiments. The challenge is to reduce non-specific interactions without impairing antibody-epitope binding. Causes of non-specific staining include interactions of the primary and secondary antibodies with serum proteins, ionic interactions between antibodies and tissues, and interactions with endogenous molecules capable of affecting the IHC detection system used. These issues can result in high background and an inability to visualize the antigen of interest in its appropriate cellular location. Staining problems of this type can be addressed by blocking non-specific interactions using a blocking reagent. These steps are performed prior to incubation of the sample with the primary antibody.

Preventing Non-specific Hydrophobic Interactions

Although hydrophobic interactions play an essential role in epitope-antibody binding, these forces can also promote non-specific binding. Most proteins have some degree of hydrophobicity due to the neutral side chains of several amino acids. Tissue incubation with heat-inactivated normal serum or bovine serum albumin (BSA) is a common procedure used to reduce non-specific hydrophobic binding. Selection of the type of normal serum is important to prevent interactions with the primary or secondary antibodies, or with the tissues/cells being stained. For example, goat serum would not be advised as a blocking reagent for use with a goat-derived primary antibody. Instead, a serum identical to the host animal of the secondary antibody or from an unrelated species is recommended. BSA and non-fat dry milk are also frequently used as blocking reagents. One of these reagents is typically included in the diluents for the primary and secondary antibodies. The addition of non-ionic detergents including 0.3% Triton X-100™ or Tween 20™ can also reduce non-specific hydrophobic interactions.

Blocking Non-specific Binding with Serum. A. CD14 was detected in paraffin-embedded human tonsil tissue using anti-human CD14 biotinylated affinity-purified polyclonal antibody (Catalog # BAF383). Tissue was subjected to antigen retrieval using the Basic Antigen Retrieval Kit (Catalog # CTS013). Tissue was stained using high sensitivity streptavidin conjugated to HRP (HSS-HRP) and DAB, and counterstained with hematoxylin (blue). B. Non-specific background staining is markedly reduced in a parallel experiment which included a blocking step using animal serum for 15 minutes at room temperature prior to incubation with the primary antibody. HSS-HRP and animal blocking serums are included in all R&D Systems Cell and Tissue Staining Kits.

Remote license server via ssh tunnel

posted Aug 6, 2019, 8:48 PM by Danny Xu

1: what’s the hostname of your campus Mathematica license server? Something like ls01.oregonstate.edu, I’m going to call it MY_LICENSE_SERVER below.

2: what’s the port number for the campus Mathematica license server? Something like 27000, I’m going to call it LS_PORT below.

3: what’s the internal port number for the Mathematica license server? Might be something like 37000, I’m going to call it INTERNAL_PORT below.

4: what’s the hostname of a system at your campus you can ssh into from off campus (specifically Bridges)? This system does not have to have Mathematica installed, but does need to be able to see the Mathematica license server. This has to be exposed to the Internet, no VPNs allowed for this method (others might know other alternatives). I’m going to call it SSH_HOST below.

You should be able to find items 1-2 from whatever Mathematica license file or environment variable you normally use. Item 3 is not as easily found, but whoever runs your campus Mathematica license server can find it in their FlexLM files on that server. Item 4 is up to you and others at your campus.

Once you’ve know all four items above, you should be able to log into Bridges, and then run:

  ssh -N username@SSH_HOST -L LS_PORT:MY_LICENSE_SERVER:LS_P
ORT -L INTERNAL_PORT:MY_LICENSE_SERVER:INTERNAL_PORT &

Once that’s done and in the background, you’ll have an ssh tunnel connecting LS_PORT and INTERNAL_PORT on the local Bridges node to LS_PORT and INTERNAL_PORT on your campus license server.

You should be able to set a license file environment variable for Mathematica to point to the Bridges end of the tunnel. Not sure what environment variable is specific to Mathematica, but many programs will fall back to using LM_LICENSE_FILE. In that case, if you’re using bash on Bridges, you can run:

  export LM_LICENSE_FILE=INTERNAL_PORT@localhost

before running Mathematica.

[1] https://software.intel.com/en-us/forums/topic/500873

AWS

posted Jul 24, 2019, 10:37 AM by Danny Xu

A few general and Texas-specific points:

- You can buy different levels of support with different SLAs. Without paid support you are on your own.
- In terms of purchasing and billing aggregation, there are several companies that will do that for you. You might check with your local AWS rep (probably Sylvia Herrera-Alaniz.) 
- Texas DIS MAY have a master purchasing agreement with AWS, which would be one approach to get UTSA Purchasing to make it easier for you to purchase AWS services.
- If you have good centralization of purchasing for AWS, I2 and AWS academic egress waiver programs will be relevant. If everyone uses their own or departmental purchase cards then aggregation of usage is nearly impossible and therefore no way to apply a waiver.


We took a dive into AWS 12-18 months ago primarily for storage with a few researchers and library electronic archives.  Tech support and our account rep have been responsive to our needs.  We utilize the Texas DIR agreement and the egress waivers.  We get one invoice with all the departments listed and their associated costs making it easy monitor usage and chargeback. 

=======================

At Oregon State we have done the same.

We contract direct with AWS, not through a reseller, but get the same
egress waiver.

We utilize the AWS structure of "Orgs" (Organizations) to roll up all
costs from our individual AWS accounts in to a single payer account. We
then distribute charges to each of the Oregon State Univ fund indexes on a
monthly basis.

We front-end the AWS console with our SSO to not require separate
username/passwords for AWS console access.

We do not add in a tax to manage this service for researchers which has
helped make it a popular option.

======================================

Use ScaleX https://www.rescale.com and AWS for all of their HPC needs: to give me access to resources that were identical to theirs without letting me in their private network. They would create different instances for each HPC software instead of fiddling with modules etc. It was very convenient and easy to use for non-HPC experts

====================================

On spot pricing: from (our former HPC director) Amy Apon  https://pdfs.semanticscholar.org/5956/5abe21878ff34f7dcf297fccc878d44a161d.pdf
Seems to make sense for large embarrassingly parallel problems.

For regular cloud pricing, there was a paper at Henry's ACIREF session last year http://www.oscer.ou.edu/acirefvirtres2018_talk_cloudvonpremise_wells_20180807.pdf .  You could change the assumptions- power,space, staffing, etc., but the conclusion is roughly that cloud makes economic sense for centers with O(50) nodes and down, and does not at O(350) nodes and up.  
Cloud vs On-Premise: Explaining Pros & Cons Jason Wells, MDY Senior Research Computing Consultant. Bentley University. Waltham, Massachusetts
We find our (heavily utilized) core-hour cost is a lot cheaper than regular Amazon prices.

Data Backup to Box

posted Jul 24, 2019, 10:18 AM by Danny Xu   [ updated Jul 24, 2019, 10:25 AM ]



  • We use Google drive for the large files.  5TB max filesize, but they throttle upload speed if you exceed 750 GB in a day.  Fine for archive, but not for analysis.     I’ve seen 20+ MB/sec on transfers, but for more than 750GB the daily limit  slows this down.     This is fine for archive, which is important, but not for analysis.
  • We also have the Box agreement here at OSU.  The 15GB size limit is a pain. We recommend using Box as backup and not for active data analysis.  We also found out that there is a limit to unlimited data     *Storage Used*  909.5 TB of Unlimited
  • At Northwestern we have the same Box agreement. Although the service is for unlimited storage. the 15GB file size limit is definitely making large transfers very difficult for our users.
  • ISU (Iowa State) offers Google Drive and Box with unlimited storage, buteither the filesize of transfer rate is limited so that this does not look like a local filesystem.

Box is actually fairly fast (we have gotten over 500 MB/sec. with parallel streams from a parallel filesystem) when large numbers of files are transferred, but the files cannot be large (we paid to get 15GB filesize limits, but the standard is 5GB limit).

==============File Split and Backup to Box===========================



FTPS is a bit of a pain, but it works after setting a local, non-federated, password for the Box user's account. Box is a great place to archive old project directories, or share out data to third parties.  We do use Rclone for this.  Highly recommended.

A few tips on using Rclone with Box...  Watch our for the 5GB file limit.  You can get around this with tar and the Linux split utility.  I prefer zip then zipsplit for end-users, though.  Don't try to upload thousands individual files.  The overhead of statting and comparing each file is stupendous.

  Something like:
  zip -v -r DIR dirtozip
  zipsplit -n $(( 4 * 1024 * 1024 * 1024 )) DIR.zip

 
  If you really want to get fancy, submitting all the commands through the scheduler, using tar and split...

  mkdir /home/bob/project01-archive

  qsub -N tar_project01 -o /home/bob/.config/rclone/ -m e -M bug@wharton.upenn.edu -j y -b y "tar -cvf - /home/bob/project01 |xz -1 - |split -b 5000000000 - /home/bob/project01-archive/project01.tar.xz."   

  qsub -N box_project01 -o /home/bob/.config/rclone/ -m e -M bug@wharton.upenn.edu -j y -b y "rclone copy -u -v --transfers 8 /home/bob/project01-archive Box:HPCC/project01-archive"

  rclone ls Box:HPCC/project01-archive

  rm -rf /home/bob/project01 /home/bob/project01-archive

=========================================

Globus now supports Box. That might help with some of the issues raised here, like federated auth and getting data on and off HPC systems.

https://www.globus.org/press-releases/globus-announces-integration-box-cloud-content-management


Alignment in ezCADD/NGL

posted Jul 2, 2019, 3:05 PM by Danny Xu

Open the console of your browser. (Here is how to open it in different browser: https://kb.mailster.co/how-can-i-open-the-browsers-console/)
1. Load chain A of 1y6q to ezCADD main window (attached) => stage.compList[0]
2. Load chain B of 1nc1 to ezCADD main window (attached) => stage.compList[1]
3. Align chain A of 1y6q to chain B of 1nc1 => NGL.superpose(stage.compList[0].structure, stage.compList[1].structure, false)
4. Update the position of chain A of 1y6q => stage.compList[0].updateRepresentations({ 'position': true })

So the commands in Blue background above should be pasted in console.

Outcome server windows 10 remote desktop using rdpwrap

posted May 31, 2019, 9:06 AM by Danny Xu   [ updated May 31, 2019, 9:13 AM ]

RDPWrap on 10.0.17134.706


Edit:  C:\Program Files\RDP Wrapper\rdwrap.ini

Hi, it worked for me. Add this to the end of your file C:\Program Files\RDP Wrapper\rdwrap.ini
Then restart the Remote Desktop services (run services.msc as Admin):

[10.0.17134.706]
LocalOnlyPatch.x86=1
LocalOnlyOffset.x86=ADAB8
LocalOnlyCode.x86=jmpshort
LocalOnlyPatch.x64=1
LocalOnlyOffset.x64=92521
LocalOnlyCode.x64=jmpshort
SingleUserPatch.x86=1
SingleUserOffset.x86=36B1C
SingleUserCode.x86=nop
SingleUserPatch.x64=1
SingleUserOffset.x64=1511C
SingleUserCode.x64=Zero
DefPolicyPatch.x86=1
DefPolicyOffset.x86=33579
DefPolicyCode.x86=CDefPolicy_Query_eax_ecx
DefPolicyPatch.x64=1
DefPolicyOffset.x64=10E78
DefPolicyCode.x64=CDefPolicy_Query_edi_rcx
SLInitHook.x86=1
SLInitOffset.x86=475DD
SLInitFunc.x86=New_CSLQuery_Initialize
SLInitHook.x64=1
SLInitOffset.x64=22F5C
SLInitFunc.x64=New_CSLQuery_Initialize

[10.0.17134.706-SLInit]
bInitialized.x86 =CBF38
bServerSku.x86 =CBF3C
lMaxUserSessions.x86 =CBF40
bAppServerAllowed.x86 =CBF44
bRemoteConnAllowed.x86=CBF48
bMultimonAllowed.x86 =CBF4C
ulMaxDebugSessions.x86=CBF50
bFUSEnabled.x86 =CBF54

bServerSku.x64 =F1378
lMaxUserSessions.x64 =F137C
bAppServerAllowed.x64 =F1380
bInitialized.x64 =F2430
bRemoteConnAllowed.x64=F2434
bMultimonAllowed.x64 =F2438
ulMaxDebugSessions.x64=F243C
bFUSEnabled.x64 =F2440

Is it possible to use a threading adapter (e.g. M25 to RMS) and use a Nikon lens on the EVOS?

posted May 15, 2019, 10:28 AM by Danny Xu   [ updated May 15, 2019, 10:30 AM ]

The short answer is that Nikon and Olympus objectives are NOT typically compatible on the same optical system (there are a few exceptions). The key reason is that there will be one shared tube lens in the optical path. Nikon is optimized for a 200mm tube lens focal length (modern objectives) and Olympus is optimized for a 180mm tube length. So the optical performance will be sub-par for the Nikon objective because the tube lens focal length is incorrect. The other key thing is that Nikon objectives are built on a 60mm parfocal distance (the distance from the in focus sample to the back of the objective), and the Olympus/AMG objectives are built on a 45mm parfocal distance. This will make a HUGE impact if switching between Nikon and Olympus objectives for focusing, since they will always me a minimum of 15mm out of focus, which is a giant length in microscopy. In an automated system, it also creates the risk of crashing, since the software will not know that the Nikon objective is a 60mm parfocal lens.

Some Zeiss lenses can be mixed and matched with Olympus objectives, because they are close enough in tube length. However, one drawback of some modern Zeiss objectives is that some of the optical corrections (like Chromatic Aberrations) are fixed in the tube lens, NOT the objective itself. Olympus corrects everything in the Objectives. That means that a Zeiss objective with an Olympus or AMG tube lens will be inferior optically because chromatic aberration will be more pronounced.

Confocal and Widefield Image Processing

posted May 7, 2019, 7:37 PM by Danny Xu   [ updated May 7, 2019, 8:35 PM ]

Z-Stack Step Size


Microscope Calibration

Have you gone through the entire process of aligning the optical path? Are your phase plate and annulus properly matched? Is your Kohler illumination aligned? Are your samples sitting flat on the stage? Is your camera in the correct alignment in the optical port?
The microscope itself is professional grade. You should be able to take clear images in any mode so long as it is in working order.

Image Overlay

3D reconstruction of 2D confocal image stacks

Chimera software (http://www.cgl.ucsf.edu/chimera/) for 3D visualisation of confocal stack (after processing with ImageJ).

Amira for 3D visualization. It is a very expensive software. But they generously enable all the features for the trial version.
ImageJ (Fiji, just a new name for ImageJ) has many plugins for 3D visualization like 3D Viewer, Volume Viewer.


Bitplane Imaris vs. Amira
That depends on what kind of analysis do you need mostly. Amira is good at 3D/4D visualization, segmentation; you can easily generate workflow and apply to other dataset. Imaris has lots of isolated modules you can buy for particular applications, such as deconvolution, co-localization. Imaris can also connect to MATLAB, if my memory is correct. If you do not really need some particular functions/algorithms of Amira or Imaris, I suggest you start from Imagej or Fiji. It's free and has covered most common image processing and analysis algorithms, and highly flexible and extendable, if you are little background of programming.

Cell Counting with Imaris

Deconvolution

There are some for ImageJ, but it is suggested that the best bling algorithm is implemented in commercial software AutoQuant. The list of interesting blind and nonblind algorithms can be found here http://deconvolve.net/DNLinks.html
The one of blind methods I like most among mentioned is LASIP.
But why do you prefer blind deconvolution? Nonblind ones usually give better results and are less computational intesive. The best among commercial is Huygens Suite (week trial available in www.svi.nl), the best among freeware is COSMOS (http://cirl.memphis.edu/cosmos.php , new release will be ready in several weeks). For WF microscopy the mentioned ones give very high image quality improvement.



The point spread function (PSF) is the hardest to get. Without a good PSF deconvolution is meaningless.
I am skeptical of blind deconvolution in general (estimating the entire PSF image using an iterative process)


First create the PSF-file using your exact settings (mounting, oil, objective, NA,...) and use this for the deconvolution.

One generally deconvolves z-stack images. You can first acquire a z-stack of a stuck bead under the same magnification to generate the PSF. Open the image z-stack after this and then go to the 3D-Deconvolve function. Select the image stacks there: one sample stack and the other PSF genrated. Play with the parameters and you will get your deconvolved image from this

"Two plugins can be used in ImageJ to perform 3D deconvolution, DeconvolutionLab and Parallel Iterative Deconvolution.
They both need a stack containing the PSF, they are based on iterative algorithms, that is to say they first compute the estimated original signal. Then this estimated original signal is convolved with the PSF, so it should reproduce the deformation induced by the system and give the actual image. Different algorithms are then used to minimise this difference. A commonly used algorithm in fluorescence microscopy is Richardson-Lucy".


Free:  ImageJ/Image2, FIJI, ICY


co-localization plugins are available for the open source java application ImageJ (http://rsbweb.nih.gov/ij/) and its various distributions, including Fiji (http://pacific.mpi-cbg.de/wiki/index.php/Fiji). Two plugins that implement all the co-localization methods described above are JaCoP (ImageJ) and Coloc_2 (Fiji)."

EpiDEMIC plugin on icy (http://icy.bioimageanalysis.org/). It is a blind deconvolution (ie no need of a PSF) algorithm for epifluorescence

The implication that "ImageJ is not appropriate for deconvolution" is not correct. ImageJ/Icy and other open source programs can produce results as good or better as commercial deconvolution if used properly. In fact in the most recent Deconvolution Grand Challenge, one of Ferreol's algorithms beat all the commercial entries (the best commercial entry was actually the Olympus implementation by David Biggs). In a recent paper, several algorithms from Deconvolutionlab2 were tested against Huygens and produced comparable results

I encourage anyone interested in ImageJ and/or Icy deconvolution implementations to post questions on the respective listservs and forums, and share images. If you interact with the developers and community you will be able to obtain very good results.



Commercial:  Huygens (SVI, Inc), Imaris (Bitplane), Autoquant X (Media Cybernetics) and Volocity (Perkin Elmer).

EVOS LED Light Cube for DASPEI

posted Apr 4, 2019, 10:25 AM by Danny Xu   [ updated May 7, 2019, 2:01 PM ]

DASPEI dye (λEx/λ Em = 461/589 nm). Our EVOS FL system (AMAFD1000) contains these 4 light cubes:

AMEP-4652 (RFP, Ex: 531/40 Em: 593/40) 
AMEP-4650 (DAPI, Ex: 357/44 Em: 447/60)
AMEP-4651 (GFP, Ex: 470/22 Em: 525/50)
AMEP-4669 (CFP-YFP EM     Ex: 445/45 Em: 542/27)
AMEP4660 QDot 585 (Ex: 445/45 Em: 586/20)

FM1-43 479 598
YOYO-1 / YO-PRO-1 491 509
Cy3   550 570
DsRed (Red Fluorescent Protein) 558 583
Texas Red® / Texas Red®-X 595 613


Courtenay@ThermoFisher: The peaks of DASPEI do not fit commonly available filters, but the dye spectra is broad enough that you should be able to use the RFP filter cube with this dye. 

AMEP4652 is the RFP cube that has Ex 531/40  Em 593/40 and is the only cube you have that will work with DASPEI. The RFP 531/40 nm excitation filter will just catch the upper edge of the excitation spectra and the 593/40 nm emission filter matches the emission peak very well. 

531/40 means 531 +/- 20 nm, or 511 -551 nm.  The excitation range is not ideal for DASPEI but there is enough excitation of the dye at 511 to about 530 nm, that this filter should work OK.  The 593/40 emission filter is a perfect match for DASPEI.

The best match, if you wanted to purchase a cube, would be the AMEP4660 QDot 585 cube with 445/45 excitation and 586/20 emission.  Other cubes that could be used are AMEP6470 Acridine orange cube (442/46, 488LP) and the AMEP4666 QDot general cube (445/45, 525-800)
 

XAMPP

posted Feb 7, 2019, 2:24 PM by Danny Xu

 Auto installed Apache, PHP, and Perl, MySQL, can use MariaDB already installed.

set up phpMyAdmin to automatically log in as user. I  also created a database user that has full control over (minus grant and lock tables).

XAMPP has a very well designed configuration tool so if we do need to update anything it should be super easy.

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