Electronics and Equipment

Electronics and Equipment kdorfman Wed, 10/19/2011 - 16:27
isotemp_calibration.xlsx
isotemp_plug.jpeg

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 home

Getting 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:

    • /export/quantbiol
    • /export/Bioimaging
    • /export/mboms

  • 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)

Voilà!

Printing

Printing margaret Wed, 10/12/2011 - 15:35

Go to the Biology, BCRC web site. Hit drop down menu for Undergraduate, print release ISB.

Resources-print release.

Sign in, select the printer, release, print.

Printers are Xerox ColorQube 8570

264 Nifiloli

360 Nupani

364 Nukapu

368 Ngawa

Inks (2 packs) from Gov Connection $138.37

yellow 108R00928

cyan 108R00926

magenta 108R00927

black 4 pack 108R00930

Xerox 108R00966 Rainbow pack (1 each CYMK) from Spare Parts Warehouse @$74.95

Printing in Biology ISB space 2019.pdf

Screen Capture

Screen Capture rootlet Fri, 04/02/2010 - 14:46

You can capture still images of videos of anything on the computer screens that Biology supports.

Capture Stills

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.

Capture Video

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 &
   [1] 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
   
   [1]+  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-radmind

Updating 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 equipment

Major equipment kdorfman Wed, 07/15/2009 - 20:57

Autoclaves:

  • 261,
  • 361
    • Consolidated Sterilizer
    • Model SR-24C-PB
    • SR 071608

Dishwashers in 261, 361 (Belimed WD 230 SN 998360086004)

Freezers (-20) in 366A, 262A

Freezer (-80) in 262A, 364

Percival Incubators in 364 (originally from the Markstein lab) I36NL SN17922. 04. 12I

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

Belimed WD 230 manual
Sanyo -80 manual
Percival Intellus manual

Convection Oven

Convection Oven margaret Fri, 10/14/2011 - 16:01

Motic Camera & Software

Motic Camera & Software margaret Wed, 10/12/2011 - 16:03

Plug your camera into a USB port on the back of the computer

Open Finder

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
using_the_motic_camera.docx
motic_cam_in_situ.jpg
putting_adapter_on_motic_cam.jpg
putting_motic_on_microscope.jpg

Projectors

Projectors 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 Scopes

Dissecting Scopes kdorfman Fri, 12/21/2018 - 19:34
Room base head how many
264 flat 445 1
mirror 445 4
360 flat 445 12
mirror trinoc (63X) 1
flat no head 6
364 flat no head 1
flat 445 11
mirror 445 3
368 mirror 445 6 (VASCI = 5)
mirror 645 17
mirror 745 2

Optima Plate Reader

Optima 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:
Setup
Program configuration
preferences
define format

Set Preferences before running a script! See p 28 of user manual ii, below.

Setup > Program Configuration > Define Format > Filename and Path

File info

Overwrite, append, make new file with same name + number

Header:

  • 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. (!?!)

Style

  • 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)

Script mode

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
340 520
485 570
492 590
530 620
544
584
595
optima.docx
0413b0001i_operating_manual_fluostar_polarstar_lumistar_optima.pdf
0413f0010a_software_manual_optima_part_i.pdf
0413f0011a_software_manual_optima_part_ii.pdf
0413f0016a_software_manual_optima_part_iiia.pdf
0413f0013a_software_manual_optima_part_iiib.pdf
0413f0014a_software_manual_optima_part_iv.pdf
0413f0015b_quick_guide_optima.pdf
bmg_filter_overview_scan_7a.xls

Plate Reader Programs

Plate 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

or

On Pstar2, even though the files say Polar star 1):

Desktop/This PC/Local Disc (C:)/Users/Public/Public Downloads/polarstar1/PS1_Protocols

Program Layout method ex em vol
BUG OD 1 A&B Abs 595 . 250
BUG_FLUOR 2 A:H FL 486 520 .
BUG_OD_SHAKE 3 A:H ABS 595 . 200
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 .
REPEATAILITY_FL 8 A:B FL 485 520 .

Script for overnight growth and fluorescence

helpful video from BMG

  1. Lab 3.1 (2022) counting bacteria: std curve OD vs population density ↩︎

  2. Lab 4.2 (2022) lac operon shake cells, then read OD for overnight growth curves – part of script “Grow&Glow” ↩︎

  3. Lab 4.2 (2022) lac operon after BugOD Shake,read FL for overnight growth curves– part of script “Grow&Glow” ↩︎

  4. Lab 1.2 serial dilution & plate reader sensitivity ↩︎

  5. Lab 1.2 pipetting consistency (ABS) ↩︎

  6. Lab 1.3 serial dilution; absorbance of fluorescein; std curve ↩︎

  7. Lab 1.3 serial dilution; fluorescence of fluorescein; std curve ↩︎

  8. (Lab 1.2) pipetting consistency (FL) not used in 2022 ↩︎

Script for lac operon lab

Script 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!

Location: C:\Users\Public\Downloads\PS1_Protocols\E_Coli_Grow&Glow.btc

(or PS2)

Multiple measurements for 17.5 hours

;absorbance and fluorescence

st1:="BUG_OD_SHAKE"

st2:="BUG_FLUOR"

for i:=1 to 70 do begin

ID1:="BOD1"

ID2:= <protocol>

ID3:=<method>

R_Run "<st1>"

ID1:="BFL1"

ID2:= <protocol>

ID3:= <method>

R_Run "<st2>"

wait for 13 m

end;

beep

(Names for PS2 = BOD2, BFL2)

Other digital cameras

Other digital cameras kdorfman Mon, 01/15/2018 - 20:28

OptixCam

(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

AmScope

10MP Windows & Mac OS Compatible Microscope Camera + Calibration Kit SKU: MA1000-CK

(download software from amscope)

http://www.amscope.com/software-download#tucs1