Electronics and EquipmentElectronics and Equipment kdorfman Wed, 10/19/2011 - 16:27
Computers, servers, etc.Computers, servers, etc. kdorfman Wed, 08/19/2009 - 16:55
The OIT wireless network is installed throughout the ISB. Make sure you have turned on AirPort or your wireless receiver, and sign in using your OIT account username and password.
Set up your bcrc account here: https://wahoo.nsm.umass.edu/passwd/
Computers that are plugged into the network in the biology labs are on the BCRC server; sign in as yourself (after you have set up your account).
Getting to Wahoo files from homeGetting to Wahoo files from home kdorfman Sat, 10/29/2011 - 17:15
- Get and install Filezilla (see here).
- Open FileZilla
- Open Site Manager from the File Menu:
- Host name: wahoo.nsm.umass.edu
- Username: your bcrc username
- password: your bcrc password
- port: 22
- Protocol: SFTP
- Logon Type: ask for passwork
- User: your BCRC username
- Click Connect
- Enter your BCRC username and password
- The first time, you get a warning about an unknown host. Check the box next to Always trust this host, add this key to the cache, and click OK
- You should be in a directory called something like /u1/home/bio/username (with your bcrc username, of course).
Clear the Remote site and type the appropriate one of these:
Enlarge the absurdly small window under the remote site bar and scroll to find your microscope folder. Move files between local and remote folders by drag-and-drop, or by right click and upload (local to remote) or download (remote to local)
PrintingPrinting margaret Wed, 10/12/2011 - 15:35
Go to the Biology, BCRC web site. Hit drop down menu for Undergraduate, print release ISB.
Sign in, select the printer, release, print.
Printers are Xerox ColorQube 8570
Inks (2 packs) from Gov Connection $138.37
black 4 pack 108R00930
Xerox 108R00966 Rainbow pack (1 each CYMK) from Spare Parts Warehouse @$74.95
Screen CaptureScreen Capture rootlet Fri, 04/02/2010 - 14:46
You can capture still images of videos of anything on the computer screens that Biology supports.
To capture still images, you can use some magic keystrokes:
Capture whole screen: Command + Shift + 3
Capture region: Command + Shift + 4 to turn cursor to cross-hairs, then select region.
There is also an application in the Utilities folder called "Grab" that will let you set some options or get images just of particular windows.
To capture video, you need to use the command-line. Videos of the entire screen are very large. You might want to use the System Preferences to set the screen resolution lower before starting to capture video. We're using the vnc2flv project. Start up Terminal (Also in the Utilities folder, but there a shortcut in the Dock). You can use two commands to start recording video. With any luck, it will be as simple as this:
First, go to the Desktop to save your work there: delfeno:~ sbrewer$ cd Desktop
Then start x11vnc: delfeno:Desktop sbrewer$ x11vnc &
You'll see a bunch of output -- once the output stops, hit return to get the prompt back, then type: delfeno:Desktop sbrewer$ flvrec.py
It will record video and save it in a file on the Desktop until you tell it to stop. You tell it to stop by typing Control + C. You should end up with a file on the Desktop called something like "out201004020900.flv". You can open this file using VLC to watch the video. To import the file into iMovie, you need to transcode the file into something iMovie understands: delfeno:Desktop sbrewer$ ffmpeg -i out201004020900.flv -sameq out201004020900.mov
The .mov file can be imported into iMovie, where you can edit the clip, add a sound-track, or combine with other videos.
Below is a complete session so you can see all the parts put together.
Last login: Fri Apr 2 09:21:58 on ttys006 delfeno:~ sbrewer$ cd Desktop delfeno:Desktop sbrewer$ x11vnc &  37779 delfeno:Desktop sbrewer$ 02/04/2010 09:44:17 MacOS X: set -connect file to /tmp/x11vnc-macosx-remote.sbrewer ############################################################### #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@# #@ @# #@ ** WARNING ** WARNING ** WARNING ** WARNING ** @# #@ @# #@ YOU ARE RUNNING X11VNC WITHOUT A PASSWORD!! @# #@ @# #@ This means anyone with network access to this computer @# #@ may be able to view and control your desktop. @# #@ @# #@ >>> If you did not mean to do this Press CTRL-C now!! <<< @# #@ @# #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@# #@ @# #@ You can create an x11vnc password file by running: @# #@ @# #@ x11vnc -storepasswd password /path/to/passfile @# #@ or x11vnc -storepasswd /path/to/passfile @# #@ or x11vnc -storepasswd @# #@ @# #@ (the last one will use ~/.vnc/passwd) @# #@ @# #@ and then starting x11vnc via: @# #@ @# #@ x11vnc -rfbauth /path/to/passfile @# #@ @# #@ an existing ~/.vnc/passwd file from another VNC @# #@ application will work fine too. @# #@ @# #@ You can also use the -passwdfile or -passwd options. @# #@ (note -passwd is unsafe if local users are not trusted) @# #@ @# #@ Make sure any -rfbauth and -passwdfile password files @# #@ cannot be read by untrusted users. @# #@ @# #@ Use x11vnc -usepw to automatically use your @# #@ ~/.vnc/passwd or ~/.vnc/passwdfile password files. @# #@ (and prompt you to create ~/.vnc/passwd if neither @# #@ file exists.) Under -usepw, x11vnc will exit if it @# #@ cannot find a password to use. @# #@ @# #@ @# #@ Even with a password, the subsequent VNC traffic is @# #@ sent in the clear. Consider tunnelling via ssh(1): @# #@ @# #@ <a href="http://www.karlrunge.com/x11vnc/#tunnelling">http://www.karlrunge.com/x11vnc/#tunnelling</a> @# #@ @# #@ Or using the x11vnc SSL options: -ssl and -stunnel @# #@ @# #@ Please Read the documention for more info about @# #@ passwords, security, and encryption. @# #@ @# #@ <a href="http://www.karlrunge.com/x11vnc/faq.html#faq-passwd">http://www.karlrunge.com/x11vnc/faq.html#faq-passwd</a> @# #@ @# #@ To disable this warning use the -nopw option, or put @# #@ the setting in your ~/.x11vncrc file. @# #@ @# #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@# ############################################################### 02/04/2010 09:44:19 x11vnc version: 0.9.9 lastmod: 2009-12-21 pid: 37779 02/04/2010 09:44:19 XOpenDisplay(":0.0") failed. 02/04/2010 09:44:19 Trying again with XAUTHLOCALHOSTNAME=localhost ... 02/04/2010 09:44:19 Continuing without X display in -rawfb mode. 02/04/2010 09:44:19 macosxCG_init: initializing display. 02/04/2010 09:44:19 console_guess: file is /dev/null 02/04/2010 09:44:19 console_guess returned: map:macosx:/dev/null@1680x1050x32:ff0000/ff00/ff 02/04/2010 09:44:19 raw fb is non-regular file: /dev/null 02/04/2010 09:44:19 rawfb: macosx fb: /dev/null 02/04/2010 09:44:19 w: 1680 h: 1050 b: 32 addr: 0x1860000 sz: 7056000 02/04/2010 09:44:20 initialize_screen: fb_depth/fb_bpp/fb_Bpl 24/32/6720 02/04/2010 09:44:20 02/04/2010 09:44:20 Raw fb at addr 0x1860000 is 32bpp depth=24 true color 02/04/2010 09:44:20 02/04/2010 09:44:20 Autoprobing TCP port 02/04/2010 09:44:20 Autoprobing selected port 5900 02/04/2010 09:44:20 fb read rate: 10 MB/sec 02/04/2010 09:44:20 Manually set num_buttons to: 5 02/04/2010 09:44:20 screen setup finished. 02/04/2010 09:44:20 02/04/2010 09:44:20 WARNING: You are running x11vnc WITHOUT a password. See 02/04/2010 09:44:20 WARNING: the warning message printed above for more info. 02/04/2010 09:44:20 The VNC desktop is: delfeno.bio.mor.nsm:0 PORT=5900 delfeno:Desktop sbrewer$ flvrec.py start recording 02/04/2010 09:44:26 Got connection from client 127.0.0.1 02/04/2010 09:44:26 other clients: 02/04/2010 09:44:26 macosxCG_callback: register 02/04/2010 09:44:26 incr accepted_client=1 for 127.0.0.1:53061 sock=5 02/04/2010 09:44:26 Client Protocol Version 3.8 02/04/2010 09:44:26 Protocol version sent 3.8, using 3.8 02/04/2010 09:44:26 rfbProcessClientSecurityType: executing handler for type 1 02/04/2010 09:44:26 rfbProcessClientSecurityType: returning securityResult for client rfb version >= 3.8 02/04/2010 09:44:26 Pixel format for client 127.0.0.1: 02/04/2010 09:44:26 32 bpp, depth 8, big endian 02/04/2010 09:44:26 true colour: max r 255 g 255 b 255, shift r 24 g 16 b 8 02/04/2010 09:44:26 Using raw encoding for client 127.0.0.1 02/04/2010 09:44:26 copy_tiles: allocating first_line at size 54 02/04/2010 09:44:27 client_set_net: 127.0.0.1 0.0007 ^Cstop recording delfeno:Desktop sbrewer$ 02/04/2010 09:44:33 client_count: 0 02/04/2010 09:44:33 viewer exited. 02/04/2010 09:44:33 deleted 53 tile_row polling images. 02/04/2010 09:44:33 macosxCG_callback: unregister + Done x11vnc delfeno:Desktop sbrewer$ ffmpeg -i out201004020944.flv -sameq out201004020944.mov FFmpeg version 0.5.1, Copyright (c) 2000-2009 Fabrice Bellard, et al. configuration: --enable-libmp3lame --enable-libfaac --enable-nonfree libavutil 49.15. 0 / 49.15. 0 libavcodec 52.20. 1 / 52.20. 1 libavformat 52.31. 0 / 52.31. 0 libavdevice 52. 1. 0 / 52. 1. 0 built on Mar 31 2010 12:11:13, gcc: 4.0.1 (Apple Inc. build 5493) Seems stream 0 codec frame rate differs from container frame rate: 1000.00 (1000/1) -> 12.00 (12/1) Input #0, flv, from 'out201004020944.flv': Duration: 00:00:07.16, start: 0.000000, bitrate: N/A Stream #0.0: Video: flashsv, bgr24, 1696x1056, 12 tbr, 1k tbn, 1k tbc Output #0, mov, to 'out201004020944.mov': Stream #0.0: Video: mpeg4, yuv420p, 1696x1056, q=2-31, 200 kb/s, 90k tbn, 12 tbc Stream mapping: Stream #0.0 -> #0.0 Press [q] to stop encoding frame= 87 fps= 42 q=0.0 Lsize= 7277kB time=7.25 bitrate=8222.8kbits/s video:7276kB audio:0kB global headers:0kB muxing overhead 0.019529% delfeno:Desktop sbrewer$
Updating the computers-radmindUpdating the computers-radmind margaret Wed, 10/12/2011 - 15:41
Using the apple drop down, logout.
When the user name and password comes up, type in: radmind, enter, enter.
The computer will update.
Important! Connect the laptops to an etherternet cable to run radmind.
Do not run from wireless connection!
Major equipmentMajor equipment kdorfman Wed, 07/15/2009 - 20:57
Autoclaves in 261, 361
Dishwashers in 261, 361 (Belimed WD 230 SN 998360086004)
Freezers (-20) in 366A, 262A
Freezer (-80) in 262A
Plant tissue culture incubator in 373
2 Arabidopsis growth chambers in 373
Convection Oven (cord broken summer 2022)
Leica cryostat CM1859 S/N 5814
- in 264 (was used in histology and as emergency cryostat for various research labs)
- maybe moving to Morrill equipment room
Minus 80 (from Biochem storage) SANYO VIP -86 (SN #41115285) in 364
Convection OvenConvection Oven margaret Fri, 10/14/2011 - 16:01
Detergent for DishwasherDetergent for Dishwasher margaret Wed, 10/12/2011 - 17:09
Order from Fisher Scientific: Catalog Number-04319B Detergent Liquid Nalgene L900
Plant growth chambersPlant growth chambers kdorfman Tue, 10/27/2020 - 16:45
Conviron Adaptis A1000
2 set up for Arabidopsis:
1 set up for tissue culture 089136
Motic Camera & SoftwareMotic Camera & Software margaret Wed, 10/12/2011 - 16:03
Plug your camera into a USB port on the back of the computer
Go down to applications
Select Motic Images Plus
Motic Images Plus
With camera attached you will see an image.
If not try:
File New Live Video
2021 (June) Motic inventory2021 (June) Motic inventory kdorfman Tue, 06/08/2021 - 20:19
|5.0||2500||1||very slow on dissecting trinoc in 360|
|2.0||2300||9||4||(9 including 1 on trinoc in 360)|
ProjectorsProjectors kdorfman Wed, 06/17/2009 - 14:50
There are two different kinds of projectors in the ISB biology/biochemistry lab wing:
Rooms 360 and 364 have the higher quality projectors.
In 360, the projector is turned on via the Crestron. Hold down the video button until the projector turns on, then press the pc button to switch to your computer.
The instructor's computer, at the central microscope, has a mini-DVI to DVI adaptor connection to the cable running up the central pole.
For best resolution from the instructor's computer, log in as bcrc, then go to system preferences>displays, and pick 1344 x 1008 on the projector. Switch to the monitor, and go to arrangement, set it to mirror images. Set the resolution to 1344 x 840.
Use the remote control (in the drawer at the window side of the room labeled "remote control") to turn the projector on and off if the Crestron doesn't seem to work.
To connect to the projector via VGA, use the connector on the Crestron.
To turn the projector off, press the video button until the light blinks.
In 364, there are two connections to the projector: under the window to the right of the screen (#2), and at the desk behind the projector (#1). Connecting to the jack at the window overrides the signal from the jack at the desk. The front jack should also give you a better image.
In room 264, there are two projector jacks: under the window to the right of the screen (#2), and at the desk behind the projector (#1). The jack at the front gives you better video quality, but if you need sound, you need to use the jack by the desk.
To reset the projector if is claiming input from video instead of computer, use the remote (in a labeled drawer near the jack at the front of the room). Or unplug the projector (the white cable from the projector to the ceiling outlet), wait a minute, then replug it.
Dissecting ScopesDissecting Scopes kdorfman Fri, 12/21/2018 - 19:34
|368||mirror||445||6 (VASCI = 5)|
Nikon E200Nikon E200 kdorfman Thu, 08/28/2014 - 16:46
To clean and troubleshoot:
make sure lamp housing is all the way in
make sure swing-out condenser is all the way in or out.
check underside of ocular head for fingerprints
pointer goes under the viewfield ring
See manual here: http://www.micropticsl.com/wp-content/uploads/2013/09/nikon_e200_manual…
Optima Plate ReaderOptima Plate Reader kdorfman Tue, 01/17/2017 - 19:12
Link to Programs here
sign in to the "student" account
user = .\student pw = student@ISB364
Find Optima Control in the start menu
Folders icon pinned to taskbar
Data files go to: This PC > Local Disc (C:) > users > student > documents
(also to backups)
Find protocols to import in: This PC > Local Disc (C:) > users > Public > Public Downloads > PS1_Protocols
Plate IDs (in the run menu)
ID1 is file name. Be sure to give a file name
To get the meta data on the output csv file:
Set Preferences before running a script! See p 28 of user manual ii, below.
Setup > Program Configuration > Define Format > Filename and Path
Overwrite, append, make new file with same name + number
- no header - just the data - useful for files that have to be compiled
- long header includes wavelength - just the right amount of info (USE THIS)
- full header (Ex, Em wavelength, date, time, etc) way too much info
- short header does not include wavelength
- Danish headers writes the file name next to the row ID. (!?!)
- Table: no well numbers, or wavelength indicators, etc. Just the results in plate layout form.
- Table with well numbers: puts the well IDs next to the reading (Very hard to read)
- Table with well numbers (only measured wells)
Table with well numbers in plate layout style: USE THIS
List (Literally, a list. no plate info. all values in one column)
List with well numbers
A B 1 A01 10 2 A02 12 3 A03 11 4 A04 13
List with well numbers (only measured wells): puts a - for a skipped well)
- List sorted by wells (all cycles in one row, chromatics in separate blocks)
- List sorted by wells with well numbers
- List sorted by well numbers (only measured wells)
- List sorted by wells (all cycles/intervals/channels/chromatics in one row)
- List sorted by wells 2 " " " (only measured wells)
For i = 1 to 72 This is the counter
id 1 = "BOD1" BOD1 is the file name
id 1 = "BOD1" i makes a separate file for each run, called BOD1_1. BOD1_2 etc.
|Excitation filters||Emission filters|
Plate Reader ProgramsPlate Reader Programs kdorfman Thu, 10/13/2022 - 15:20
Look for Programs here
Desktop/This PC/Local Disc (C:)/Users/Public/Public Downloads/PS1_Protocols
On Pstar2, even though the files say Polar star 1):
Desktop/This PC/Local Disc (C:)/Users/Public/Public Downloads/polarstar1/PS1_Protocols
|BUG OD 1||A&B||Abs||595||.||250|
|FL-ABS-BY-2 4||C1:2, D||ABS||485||.||150|
|REPEATABILITY 5||A & B||ABS||485||.||150|
|SERIAL2&5_ABS 6||E1-5, F:H||ABS||485||.||150|
|SERIAL2&5_FL 7||E1-5, F:H||FL||485||520||.|
Script for overnight growth and fluorescence
Lab 3.1 (2022) counting bacteria: std curve OD vs population density ↩︎
Lab 4.2 (2022) lac operon shake cells, then read OD for overnight growth curves – part of script “Grow&Glow” ↩︎
Lab 4.2 (2022) lac operon after BugOD Shake,read FL for overnight growth curves– part of script “Grow&Glow” ↩︎
Lab 1.3 serial dilution; absorbance of fluorescein; std curve ↩︎
Lab 1.3 serial dilution; fluorescence of fluorescein; std curve ↩︎
Script for lac operon labScript for lac operon lab kdorfman Mon, 10/24/2022 - 15:18
Script for overnight growth and fluorescence
Set Preferences inside the user dialog box before running a script!
Multiple measurements for 17.5 hours
;absorbance and fluorescence
for i:=1 to 70 do begin
wait for 13 m
(Names for PS2 = BOD2, BFL2)
Other digital camerasOther digital cameras kdorfman Mon, 01/15/2018 - 20:28
(uses toupview software)
Summit SK2-10X - 10.0MP - Digital USB 2.0 Microscope Camera - PC/MAC Compatible - Image Capture Software - Measuring Software (PC only) - C-Mount - 23mm Eyepiece Adapter
10MP Windows & Mac OS Compatible Microscope Camera + Calibration Kit SKU: MA1000-CK
(download software from amscope)
Zeiss scopesZeiss scopes kdorfman Tue, 01/28/2014 - 16:02
Phase scopes from Bio.
Borrowed for AnSci F13, then for QSB S14