Lab Links
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EH&S Laboratory Safety Training Cleanroom Safety Training and Orientation THz Databases | Material Databases UB Center for Computational Research (CCR) NAMD and VMD | Python (Videos) | PyMOL |
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UB Libraries Physics
- Resource Guide https://research.lib.buffalo.edu/physics
- Science Librarian: Amanda McCormick | afm33@buffalo.edu | (716) 645-0612
EH&S Laboratory Safety Training
This training is required for ALL members of the Markelz Research Group before working in the lab.
This 1.5 hour class provides basic right-to-know training on hazardous chemicals and provides instructions on how to safety handle and package laboratory wastes. All lab workers including but not limited to: research assistants, graduate assistants, post docs, visiting post docs, and undergraduate students MUST attend the training if they are performing any work in a laboratory environment.
Cleanroom Safety Training and Orientation
This training is required for all Markelz Research Group members who will also work in the Davis Hall Cleanroom.
- Request Lab Safety Training
- Schedule an Initial Cleanroom Orientation and Training Session
Complete Initial Training Certification Form (PDF) and take to session
Take this form to the Initial Orientation and Training Session to obtain an authorizing signature certifying your attendance. Scan and submit this form, along with all other required documentation for lab access, online.
Meeting Room Reservations
- Fronczak 245, 333
- Silverman 15,16,17
- Lockwood 320 (8) 520 (5)
Useful Databases
- The THz Database | http://www.thzdb.org
- The THz Spectral Database (NIST) | http://webbook.nist.gov/chemistry/thz-ir
- Protein Data Bank | https://www.rcsb.org
http://curie.utmb.edu/getarea.html
Computational Resources
UB Center for Computational Research (CCR)
- CCR Account Creation | https://idm.ccr.buffalo.edu/auth/login
- On-Demand | https://ondemand.ccr.buffalo.edu/pun/sys/dashboard
- Tutorials, Workshops and Training Documents | https://ubccr.freshdesk.com/support/solutions/articles/13000026245-tutorials-workshops-and-training-documents
- Tagging plot feature
Tag/C/N=peakname/F=0 wavename, pt#,"\\Z16\\{\"%.0f\",TagVal(1)}"
NOTES
The Selection Box:
- index % 2 == 0 - displays every other arrow
- resid % 4 == 0 - displays arrow for every fourth residue
- pbc set {48.1 53.4 64.7 92.3 74.6 116.7} -all
- supercell 1,1,1,pdb,blue
openGL cluster: Copy the following lines into emacs.bashrc
module load cuda/5.5.22
module load vmd/v1.9.2
module load gcc
module load biopython
pip install --user prody
- Python Crash Course For Beginners (1 hr 36 min) | https://www.youtube.com/watch?v=JJmcL1N2KQs
- Learn Python - Full Course for Beginners [Tutorial] (4 hr 26 min) | https://www.youtube.com/watch?v=rfscVS0vtbw
- PyMOL User's Guide (PDF | 66 pp) | http://pymol.sourceforge.net/newman/userman.pdf
Useful/FUN! Sites
- POSTER PRINTING https://buffalo.webdeskprint.com/
- All those electrical engineering questions answered! | https://www.electrical4u.com/
- BRENDA (The Comprehensive Enzyme Information System) | https://www.brenda-enzymes.org/index.php
- PhET (Interactive Physics Simulations) | https://phet.colorado.edu/en/simulations/category/physics
- RUN at Regensburg: https://www.run-regensburg.com/team
- Simulations for class: Best Physics Simulation Software for Teachers | Optics & Circuit Simulator (simphy.com)
Optics Sites
- OSA Advances in Optics and Photonics Tutorials | https://www.osapublishing.org/aop/journal/aop/tutorials.cfm
- The Optics Library | http://markelz.physics.buffalo.edu/node/411
- gwOptics ComponentLibrary | http://www.gwoptics.org/ComponentLibrary/
- Gaussian Ray Optics Simulator | https://lightmachinery.com/optical-design-center/more-optical-design-tools/gaussian-beam-propagation
- Ray Optics Simulation Tool | https://phydemo.app/ray-optics/| Chrome browser extension: Chrome Browser Extension
Protein Expression and Purification
- 600 nm OD for cell growth
- 280 nm OD for protein concentration https://novoprolabs.com/tools/protein-extinction-coefficient-calculation
- QMUL Science Alive: Protein Expression and Purification (11 min) | https://www.youtube.com/watch?v=YJr_Xtji5NE
- Aseptic Technique & Streak Plate (16 min) | https://www.youtube.com/watch?v=WYvTj6pIhbo
- PhotochemCAD™ | http://www.photochemcad.com/PhotochemCAD.html
Protein Crystallization
- https://www.youtube.com/watch?v=mDbmfyOGLIM&ab_channel=ThornLab
- pH meter manual
THz Lab Information
Lab Photos and Videos
- Dropbox (DEAD LINK, check for updates) | https://www.dropbox.com/sh/n90wpvfavinwc4q/rnC7ufHRUj
- University at Buffalo, SUNY, Department of Physics - New Faculty, New Horizons (2013, 6 min) | https://youtu.be/aysPL1VsaMY
Lab Safety Contacts
- Laser Safety (check for updates) | Frazer, Brian bmfrazer at buffalo.edu
- Chemical Safety (check for updates) | Oswald, Anthony acoswald at buffalo.edu
Contact information for the Chemical Disposal Area:
Dan Opera, Operations Manager
University at Buffalo
147 Hochstetter
North Campus
Office # 716-645-0515
danielop at buffalo.edu
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