FAQ about using the UNC Database

Overview of metadata structure in the UNC Database

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Contents

 

1. Step-by-step instructions for uploading files to the UNC servers
2. Step-by-step instructions for entering experiments into the UNC Database
   1. Loading through an HTML interface
   2. Annotating your experiment
3. Current list of users

 

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(1) Step-by-step instructions for uploading files to the UNC servers

 

Web-based tutorial illustrating how to perform a password change, transfer files via SFTP, and mount a Samba share are available at:

• https://lbg.unc.edu/docs

 

Users can download all prerequisite third-party software including SFTP client(s) via the link provided below:

• https://lbg.unc.edu/downloads

 

Users are asked to change their temporary passwords at their earliest convenience by visiting the following link:

• https://lbg.unc.edu/account

 

One example of uploading files to UNC servers

1. Open "Filezilla" (see above).
2. Enter Host: sftp://biodataex.med.unc.edu
3. Enter Username: your username. In Kohta's case, it's "ikgmk".
4. Enter Password: your password. In Kohta's case, it's "********". Note that this password is for LBG Unix account and will be different from that for the UNC data submission page (LBG Nimblegen account). If you don't have that, please request Everett (xlzhou@email.unc.edu) to issue it.  
5. Enter Port: 22
6. Press "Quickconnect"
7. You will get this kind of messages in the top status box:
8. Response:    fzSftp started

   Command:    open "ikgmk@biodataex.med.unc.edu" 22

   Command:    Pass: ********

   Status:    Connected to vienna.med.unc.edu

   Status:    Retrieving directory listing...

   Command:    pwd

   Response:    Current directory is: "/home/ikgmk"

   Command:    ls

   Status:    Listing directory /home/ikgmk

   Status:    Directory listing successful

9. Under /home/ikgmk directory, you will see "incoming" folder. Double-click it.
10. Find your data files in your local place at left hand of the window and drag them to the incoming folder at the right hand (see below). For each hybridization, please transfer two .pair files (XXXXXX_532.pair and XXXXXX_635.pair) and a .gff file.
11. You will get "Status:    File transfer successful" message in the top status box.
12. Done!! You will see the transferred files in the UNC data submission page soon after the transfer.

 

 

(2) Step-by-step instructions for use of the UNC Database

 

Vital information:

Server to upload files to (sftp/scp only): biodata.unc.edu

Experiment submission site: https://genome.unc.edu:8443/nimblegen/

 

Information regarding Loading through the HTML Interface, Batch Loading, and Annotating your experiment can be found at:

• https://lbg.unc.edu/docs

PREREQUISITES:

Add the necessary information indicated by "+" to the places listed below.

 

	Dabble DB http://modencode.dabbledb.com/	UNC database	DCC wiki
Protocol	+ (Add by yourself)	+ (Ask Everett)	+ (Add by yourself; see detail below the table) http://wiki.modencode.org/project/index.php/Category:Lieb_Group_Protocol
Antibody	+ (Add by yourself)	+ (Ask Everett)	+ (Add by yourself) http://modencode.oicr.on.ca/project/index.php/Category:Antibody
Strain	+ (Add by yourself)	+ (Ask Everett)	+ (Add by yourself) http://modencode.oicr.on.ca/project/index.php/Template:Reagent:Strain:Edit
.pair files	-	+ (Add by yourself via UNC server; see above)	-
.gff files	-	+ (Add by yourself via UNC server; see above)	-

 

Addtion of a new protocol in DCC wiki

1. Go to http://wiki.modencode.org/project/index.php/Category:Lieb_Group_Protocol
2. On top of the page you will see "Name", "Group" and "Version". Fill these fields according to the instruction below.
   1. "Name": Filename of the your protocol apart from the version information. For example, if your protocol is Worm_embryo_growth_and_harvest_vPK1.doc, type (or paste) Worm_embryo_growth_and_harvest. Underscores will be automatically removed. Always double check this field does not have version information because the wiki mistakenly and automatically add full name of the previously created protocol.
   2. "Group": Do not add anything.
   3. "Version": Add version information. For example, if your protocol is Worm_embryo_growth_and_harvest_vPK1.doc, type (or paste) PK1. Do NOT add v (version).
3. Click "Go". When the next page appears, click edit and paste your protocol including a short description. You may need to re-format the protocol.
4. Go to the bottom of the page and:
   1. Add information for "Short Description", "Species" and your "Lab".
   2. Ask Marc Perry Marc.Perry@oicr.on.ca who is responsible for our entries to fill "Protocol type", "Input type", "Output type".

     NOTE: If you mistakenly added protocol name, you won't be able to delete or modify it. Please create another protocol and ask Marc (email address above) to delete it. If you have any questions, please email Kohta ikgmk@email.unc.edu or Marc.

 

(3) List of people who have applied for login to the UNC modENCODE database:

 

Julie Ahringer ja219@cam.ac.uk ahringer

 

 

Isabel Latorre i.latorre@gurdon.cam.ac.uk ilatorre

Paulina Kolasinska-Zwierz pmk35@cam.ac.uk pkz

 

Eran Segal eran@weizmann.ac.il esegal

Noam Kaplan noam.kaplan@weizmann.ac.il nkaplan

Yaniv Lubling yaniv.lubling@weizmann.ac.il ylubling

Eilon Sharon eilon.sharon@weizmann.ac.il esharon

 

Arshad Desai abdesai@ucsd.edu abdesai

Reto Gassmann rgassmann@ucsd.edu gassmann

Ksenia Sniegowski ksniegowski@ucsd.edu sniegows

 

Susan Strome strome@biology.ucsc.edu sstrome

Andreas Rechtsteiner andreas@ucsc.edu arechtst

Thea  Egelhofer egelhofer@darwin.ucsc.edu egelhofe

 

Abby Dernburg afdernburg@lbl.gov dernburg

Hoang N Pham hnpham@lbl.gov hnpham

 

Xinmin Zhang xzhang@nimblegen.com zhang

Luke Dannenberg ldannenberg@nimblegen.com dannenbe

 

Xiaole Shirley Liu xsliu@jimmy.harvard.edu xsliu

Yong Zhang zy@jimmy.harvard.edu yzhang

Hyunjin Shin shin@jimmy.harvard.edu hshin

Tao Liu taoliu@jimmy.harvard.edu tliu

Josiah Altschuler josiah@jimmy.harvard.edu jaltschu

 

Jason Lieb jlieb@bio.unc.edu jdlieb

Chrissy Whittle cwhittle@email.unc.edu cwhittle

Sevinc Ercan ercan@email.unc.edu ercans

Morten Jensen mbjensen@email.unc.edu mbjensen

Kohta Ikegami ikgmk@email.unc.edu ikgmk

 

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Notes about the account used to upload your files

 

These accounts are Unix accounts, which provide SSH and SFTP access. When these accounts are referred to as FTP accounts, this gives users the impression that their access is limited to FTP only, which is not true. In fact, the UNC-CH fileserver does not even offer FTP access. The aforementioned servers instead offer SFTP, which is a completely different service running on a different port (port 22, _NOT_ port 21).

 

The path for the data sharing directory is "$HOME/share/modencode/For_data_sharing" (where $HOME is /home/$username). Mike has added read/write permissions to this directory for all 25 users. Note that any file put in this directory appears in the correpsonding directory of all users ($HOME/share is just a shortcut to a central share location on the server).