Setting Up Network Drives and Main Page: Difference between pages

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The laboratory has a server on which all work-related files must be stored. Before you can access these folders you must get a user ID and password from Dr. Heit.  Please follow these instructions closely in order to ensure security of our data files.  To enable access to a computer at work:
Welcome to the protocol wiki for the lab of [http://phagocytes.ca Dr. Bryan Heit], at the [http://www.uwo.ca University of Western Ontario]. This site contains the protocols, and other information, we frequently use in our lab.  Only laboratory members may edit pages, but anyone is welcome to use these protocols.  If you use these protocol, please cite us.  A link for generating citations can be found on the left side of the page.


= Windows Computer<br> =
<br> Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.<br> <br>


#Open up "My Computer" in Windows Explorer<br>  
'''''Lab members:'''''
#Click on "Map Network Drive"<br>  
 
#Select a drive, then enter \\172.18.26.41\xxx, where xxx is the share:<br>  
*To get a wiki account please contact Dr. Heit.
#*Lab Files (personal directories): HeitLab<br>  
*Log in&nbsp;(upper-right side of screen) to add/edit pages. &nbsp;
#If you want the computer to auto-mount the folder at boot, select "Reconnect at Logon"<br>  
*Please follow [[Editing|these formatting instructions]] when editing/creating protocols.
#*DO&nbsp;NOT&nbsp;DO&nbsp;THIS if the computer will be used by non-laboratory individuals<br>  
*To create a new page, [[Create new|follow these instructions]].
#Select "Use Different Credentials", then click finish<br>  
 
#*A dialogue box asking for a user ID and password should open, enter your ID and password<br>  
<br>
#If this is a personal computer you can save your password.&nbsp; DO NOT SAVE YOUR PASSWORD if the computer is no solely used by yourself, or if it is a shared computer not belonging to our lab.<br>  
 
= Index of Protocols =
 
{| width="100%" cellspacing="1" cellpadding="1" border="0" align="left"
|- valign="top"
|
===== Lab Operations =====
 
*[[Entrance Protocol|Entrance Protocol]]
*[[Exit Protocol|Exit Protocol]]
*[[Labbook Guidelines|Guidelines for Proper Use of Laboratory Notebooks]]
*[[Saving Experimental Files|Proper Saving of Experimental Files]]
*[[Setting Up Network Drives|Setting up Access to Network Drives &amp; Wiki]]
 
<br>
 
===== General Protocols =====
 
*[[Common buffers|Common Buffers]]
*[[Cell Culture Guidelines|Cell Culture Guidelines]]
*[[Bacterial Growth Media|Bacterial Growth Media]]
*[[Primary Macrophage Culture|Primary Macrophage Culture]]
*[[Freezing and Thawing Cells|Freezing and Thawing Cells]]
*[[Raw Cell Transfection|Raw Cell Transfection]]
*[[J774 Cell Transfection|J774 Cell Transfection]]
*[[Antibiotics|Antibiotics]]
*[[Antibiotic Plates|Antibiotic Plates]]
*[[Agarose Gels|Agarose Gels]]
*[[Water Bath Antibiotic Solution|Water Bath Antibiotic Solution]]
 
<br>
 
===== Phagocytosis Protocols =====
 
*[[Opsonization|Opsonization]]
*[[Preparation of Silica-Magnetic Beads|Preparation of Silica-Magnetic Beads]]
*[[Synchronised Phagocytosis|Synchronised Phagocytosis]]
*[[Phagosome Isolation|Phagosome Isolation]]
*[[Primary Human Macrophages|Primary Human Macrophages]]
*[[Labelled E coli|Labelled E coli]]
*[[Inside-out Labelling of Bacteria|Inside-out Labelling of Bacteria]]
*[[Gentamicin Protection Assay|Gentamicin Protection Assay]]
 
<br> <br>
 
|
 
===== DNA/Cloning =====
 
*[[Colony PCR|Colony PCR]]<br>  
*[[PCR|PCR]]
*[[Digests|Digests]]
*[[Ligation|Ligation]]
*[[Gibson Assembly|Gibson Assembly]]
*[[Quick 'n' Easy Competent E. coli|Quick 'n' Easy Competent ''E. coli'' (Dh5a)]]
*[[Competent e coli|Generating Competent ''E. coli'' (TFB, BL21 & ZYCY10P3S2T)]]
*[[E. coli Transduction|Transducing]] ''[[Transduction|E. coli]]''
*[[Transformation|Transformation]]
*[[Neon® Transfection System|Neon® Transfection System]]
*[[Generating Minicircles|Generating Minicircles]]
<br>
 
===== Protein work =====
 
*[[Western Blotting|Western Blotting]]
*[[Immunoprecipitation|Immunoprecipitation]]
*[[Fab preparation|Fab preparation]]
*[[Fab Purification by FPLC|Fab purification using FPLC]]
*[[Updated FPLC Size Exclusion Procedure|Updated FPLC Size Exclusion Procedure]]
*[[Coomassie Staining|Coomassie Staining]]
*[[Receptor Cross-linking and Activation|Receptor activation by Cross-Linking]]
*[[Stripping & Reprobing Blots|Stripping &amp; Reprobing Blots]]
 
<br>
 
===== Cell Biology<br> =====
 
*[[Ablation of Recycling Endosomes|Ablation of Recycling Endosomes]]
*[[Cell-Type Specific Transfection Protocols|Cell-Type Specific Transfection Protocols]]
*[[G418 & Puromycin Kill Curves|G418 &amp; Puromycin Kill Curves]]
*[[Apoptosis Detection with AnnexinV and PI|Apoptosis Detection with AnnexinV and PI]]
 
|
 
===== Microscopy =====
 
*[[Competition of Charged Molecules with Lipophilic Cations|Competition of Charged Molecules with Lipophilic Cations]]
*[[Immunostaining|Fluorescent Immunostaining]]
*[[Inhibition of Focal Contact Signaling|Inhibition of Focal Contact Signaling]]
*[[Single Particle Tracking|Single Particle Tracking]]
*[[Staining for GSD|Staining for GSD]]
*[[Reducing Photobleaching|Reducing Photobleaching]]
*[[Acid Washing Coverslips|Acid Washing Coverslips]]
*[[Live Cell FRET|Live Cell FRET]]
*[[3D Printed PDMS Chambers|3D Printed PDMS Chambers]]
 
<br>
 
===== Lipids<br> =====
 
*[[Asymmetric liposomes|Asymmetric liposomes]]<br>  
*[[Lipid Coated Bead Preparation|Lipid Coated Bead Preparation]]<br>  
*[[Lipid Extraction from Cells|Lipid Extraction from Cells]]<br>  
*[[Lipisome and Lipid-Coated Beads|Lipisome and Lipid-Coated Beads]]<br>  


<br>
<br>


= Mac OS/X Computer<br> =


#Start the ''Connect to Server'' client (in the 'Go' menu).<br>
#Enter smb://172.18.26.41/xxx, where xxx is the share<br>
#*NOTE: enter the slashes correctly - this is the opposite of windows<br> 
#Hit connect, then enter the required information.&nbsp; Workgroup is 'HEITLAB', although it should be fine to leave it blank.<br>


<br>
<br>


= Ubuntu Linux<br> =
|}
 
= Links to More Protocols =
{| width="100%" cellspacing="1" cellpadding="1" border="0" align="left"
|- valign="top"
|
===== General Protocol Sites =====
*[http://www.benchfly.com/ BenchFly] - Free Video Protocols
*[http://www.protocol-online.org/ Protocols Online] - large database of biology protocols
*[http://openwetware.org/wiki/Main_Page Open Wet Ware] - large database of open protocols
*[http://www.molecularstation.com/protocol-links/ Molecular Station] - links to many lab-generated protocols
*[http://www.thelabrat.com/protocols/ TheLabRat] - various protocols &amp; lab resourses.
*[http://www.thelabrat.com/protocols/reagents.shtml Common Buffer Recipes] @ TheLabRat
*[http://www.rsc.org/Publishing/Journals/lc/Chips_and_Tips/index.asp Chips &amp; Tips] - Microfluidics protocols
 
|
===== Free Science Ebooks =====
*[https://www.gitbook.com/book/petebankhead/imagej-intro/details Analyzing fluorescence microscopy images with ImageJ]
*[http://www.imaging-git.com/applications/bioimage-data-analysis-0 Bioimage Data Analysis] - Free registration required
|}


===== Temporary Mount:<br> =====
= Useful Links =


#Open Nautilus (file manager)<br>
{| width="100%" cellspacing="1" cellpadding="1" border="0"
#Select "Connect to Server" under the "File" menu<br>
|- valign="top"
#*Under server type select "Windows share<br>
|
#*Under server enter 172.18.26.41<br>
===== Molecular Biology Databases =====
#*Under share enter the desired share<br>
#*Under user name enter your user name<br> 
#Hit connect, enter your password when asked<br>


===== Permanently Mount:<br> =====
*[http://www.ncbi.nlm.nih.gov/gene Pubmed Gene] - Find gene information<br>
*[http://www.ncbi.nlm.nih.gov/refseq/rsg/ Pubmed RefSeq] - Find reference sequences<br>
*[http://www.uniprot.org/ Uniprot] - Find protein sequence &amp; structure<br>
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap] - Find human polymophisms<br>
*[http://www.ncbi.nlm.nih.gov/omim OMIM] - Find human gene-assocations<br>
*[http://www.pantherdb.org/ PANTHER] - Automated Protein Function Classification
*[http://useast.ensembl.org/index.html BioGrid] - Protein Interactions<br>
*[http://useast.ensembl.org/index.html Ensemble Genome] - Browse multiple genomes<br>
*[http://www.proteinatlas.org/ Human Protein Atlas] - Info onn gene exrpession, antibody's, etc<br>
*[http://www.genecards.org/index.shtml Gene Cards] - Condenced information on genes<br>
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP] - Information Hyperlinked Over Proteins<br>
*[http://www.hprd.org/index_html Human Protein Reference Database]<br>
*[http://www.wwpdb.org/ PDB] - Protein Structures<br>
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen2] - SNP Phenotype Predictor
*[http://sift.jcvi.org/ SIFT] - SNP Phenotype Predictor/db
*[http://www.timetree.org/index.php TimeTree] - evolutionary divergence database<br>  


#Get your user name ID from Dr Heit<br>  
<br>
#Make a directory to mount the share (i.e. sudo mkdir /mnt/LabServer)<br>
#*If mounting multiple shares, a folder must be created for each.<br> 
#In a terminal type "sudo gedit ~/.smbcredentials, into the editor add the two lines:<br>
#*username=MyUsername<br>
#*password=MyPassword<br> 
#sudo chown root .smbcredentials<br>
#sudo chmod 600 .smbcredentials<br>
#backup fstab: sudo cp /etc/fstab /etc/fstab-backup<br>
#sudo gedit /etc/fstab<br>
#enter at the end of fstab:<br>
#*//172.18.26.41/$xxx $mount cifs iocharset=utf8,credentials=~/.smbcredentials,uid=$UID 0 0<br>
#**$xxx = share name
#**$mount = directory on local machine to mount share
#**$UID is UID number of your account on the server 
#*Do not enter '$' in the fstab 


= Off-Campus Access =
===== Journal Resources<br> =====


Off-campus access is possible via VPN or SSH File Transfer Protocol.&nbsp; For security reasons these access methods are not available to most lab members.&nbsp; If you require this access please talk to Dr. Heit<br>
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]
*[http://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (USA)]
*[http://pubmedcentralcanada.ca/ Pubmed Central (Canada)]
*[http://scholar.google.com Google Scholar]
*[http://eigenfactor.org/ Eigenfactor] - free journal imapct scores


<br>
<br>


= Wiki Access<br> =
===== Genomics Resources<br> =====
*[http://www.gwascentral.org GWAS Central]
 
|
===== Molecular Biology Tools =====


The wiki is available from any computer, anywhere in the world.&nbsp; Simply browse to http://vmheitwiki.mni.fmd.uwo.ca<br>
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
*[http://ca.expasy.org/ ExPASy Tools]<br>
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] - PCR primer Tm calculator<br>
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter]<br>
*[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/isoschizomers.asp NEB Isoschizomers]<br>
*[http://searchlauncher.bcm.tmc.edu/seq-util/Options/revcomp.html Reverse-Complement DNA Sequence]<br>
*[http://www.insilico.uni-duesseldorf.de/Lig_Input.html Ligation Calculator]
*[http://www.addgene.org/ AddGene] - clone by e-mail!
*[http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html PattenProt] - search genomes for protein patterns
*[http://workbench.sdsc.edu/ Biology Workbench]<br>
*[http://www.ebi.ac.uk/Tools/sequence.html EMBL Sequence Tools]<br>
*[http://www.ncbi.nlm.nih.gov/projects/gorf/ NCBI ORF Finder]<br>
*[http://searchlauncher.bcm.tmc.edu/ BCM Search Launcher]<br>
*[http://swissmodel.expasy.org/ SWISS Model protein modeling]<br>
*[http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html Secondary Structure Prediction]<br>
*[http://www.predictprotein.org/ PredictProtein] - Protein structure prediction<br>
*[http://3d-alignment.eu/ STRAP] - Protein aligments with structure<br>
 
<br>
 
===== ''In Vivo'' Tools<br> =====
 
*[http://www.emouseatlas.org/emap/home.html EMAP] - Virtual mouse anatomy<br>
*[http://phenome.jax.org/ Mouse phenome database] - mouse phenotypes<br>
 
|
===== Microscopy Tools =====
 
*[http://www.microscopyu.com/ Microscopy U] - Everything you want to know about microscopes<br>
*[http://jcb.rupress.org/content/166/1/11.full Paper on Image Processing Standards] - How not to loose your job
*[http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html Fluorophore Spectra Viewer] at Life Technology<br>
*[http://www.mcb.arizona.edu/ipc/fret/ Fluorescent Spectra Database] - FRET and other
*[http://www.mcb.arizona.edu/IPC/spectra_page.htm Yet More Spectra] - from Arizona University
*[http://www.confocal-microscopy.org/ www.confocal-microscopy.org] - Data on LSM methods and equipment<br>
*[http://fiji.sc/wiki/index.php/Fiji FIJI] - <u>FREE</u> imageJ based image processing program
*[http://www.dspguide.com/pdfbook.htm Free] image processing textbook
*[http://www.archive.org/details/Lectures_on_Image_Processing Lectures on image processing]<br>
*[http://vaa3d.org/ VAA3D] FREE viewer for large 3/4/5D datasets
 
<br>
 
===== Protease Tools =====
 
*[http://merops.sanger.ac.uk/ MEROPS] - Peptidase database
*[http://www.proteolysis.org/proteases PMAP] - Proteolysis Map
*[http://casbase.org/casvm/index.html CASVM] - Caspace substrate prediction
*[http://bioinf.gen.tcd.ie/casbah/ CASBAH] - Caspase cleaveage site database
 
<br>
 
===== Lipid Tools =====
 
*[http://www.lipidmaps.org/ Lipid Maps] - Lipidomics gateway at ''Nature''
*[http://www.avantilipids.com/ Avanti Lipids] - Buy lipids
 
<br>
 
===== Chemical Tools =====
 
*[http://www.chemspider.com/ ChemSpider] - General chemistry database
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] - Chemical structure database
 
<br>
 
<br>


*User editing is currently available to registered users who are off-campus
|}


<br>
<br>

Revision as of 19:24, 1 February 2021

Welcome to the protocol wiki for the lab of Dr. Bryan Heit, at the University of Western Ontario. This site contains the protocols, and other information, we frequently use in our lab.  Only laboratory members may edit pages, but anyone is welcome to use these protocols.  If you use these protocol, please cite us.  A link for generating citations can be found on the left side of the page.


Consult the User's Guide for information on using the wiki software.

Lab members:


Index of Protocols

Lab Operations


General Protocols


Phagocytosis Protocols
DNA/Cloning


Protein work


Cell Biology
Microscopy


Lipids




Links to More Protocols

General Protocol Sites
Free Science Ebooks

Useful Links

Molecular Biology Databases


Journal Resources


Genomics Resources
Molecular Biology Tools


In Vivo Tools
Microscopy Tools


Protease Tools
  • MEROPS - Peptidase database
  • PMAP - Proteolysis Map
  • CASVM - Caspace substrate prediction
  • CASBAH - Caspase cleaveage site database


Lipid Tools


Chemical Tools




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