http://wiki.docking.org/index.php?action=history&feed=atom&title=Lab_WebsiteLab Website - Revision history2026-07-11T03:23:06ZRevision history for this page on the wikiMediaWiki 1.39.1http://wiki.docking.org/index.php?title=Lab_Website&diff=9447&oldid=prevBenrwong at 21:42, 28 June 20162016-06-28T21:42:20Z<p></p>
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</table>Benrwonghttp://wiki.docking.org/index.php?title=Lab_Website&diff=9444&oldid=prevBenrwong: Created page based on WWW & Wiki page from Lab Manual2016-06-28T20:47:25Z<p>Created page based on WWW & Wiki page from Lab Manual</p>
<p><b>New page</b></p><div>THE LAB WEBSITE (www.bkslab.org)<br />
<br />
MOVING THE LAB WEBSITE:<br />
On the<br />
<br />
UPDATING THE LAB WEBSITE: <br />
<br />
= Introduction =<br />
A little about the webpage database:<br />
As root:<br />
mysql -p<br />
use webpage<br />
show tables;<br />
+------------------------+<br />
| Tables_in_webpage |<br />
+------------------------+<br />
| Aggregators |<br />
| alumni |<br />
| ampc_binders |<br />
| ampc_non_binders |<br />
| ccp_binders |<br />
| ccp_non_binders |<br />
| compounds |<br />
| l99a_binders |<br />
| l99a_m102q_binders |<br />
| l99a_m102q_non_binders |<br />
| l99a_non_binders |<br />
| people |<br />
| publications |<br />
+------------------------+<br />
13 rows in set (0.00 sec)<br />
<br />
= Updating when staff leaves =<br />
I have only ever had to update alumni, people and publications:<br />
When some one leaves the lab you have to move them from the people table to the alumni table.<br />
describe alumni;<br />
+------------------+--------------+------+-----+---------+-------+<br />
| Field | Type | Null | Key | Default | Extra |<br />
+------------------+--------------+------+-----+---------+-------+<br />
| Last_name | varchar(100) | NO | | | |<br />
| First_name | varchar(100) | NO | | | |<br />
| Middle_name | varchar(100) | NO | | | |<br />
| Title | varchar(100) | NO | | | |<br />
| Position | varchar(100) | NO | | | |<br />
| Date_begin | int(11) | NO | | 0 | |<br />
| Date_end | int(11) | NO | | 0 | |<br />
| Current_position | varchar(100) | NO | | | |<br />
| Links | varchar(100) | NO | | | |<br />
| Link_url_1 | varchar(100) | NO | | | |<br />
| Link_name_1 | varchar(100) | NO | | | |<br />
| Link_url_2 | varchar(100) | NO | | | |<br />
| Link_name_2 | varchar(100) | NO | | | |<br />
+------------------+--------------+------+-----+---------+-------+<br />
13 rows in set (0.00 sec)<br />
Here is the steps to do that:<br />
First, for the person that is leaving you need to have their:<br />
First name<br />
Last name<br />
Title => This is their title when they left the lab<br />
Position => This is their title when they started at the lab<br />
Date begin => date begin with lab<br />
Date end => date end with lab<br />
Current position => Their title at their new job<br />
URL links => Any url links they want associated with their name (and how they want them named).<br />
<br />
== Example when staff leaves ==<br />
Here is an example of some one named Michael Mysigner who started as a Graduate student in 2006 and left in 2012 with his Ph.D. His new title is Senior Scientist and Lead Developer, etc:<br />
INSERT INTO `webpage`.`alumni` ( <br />
`Last_name` , <br />
`First_name` , <br />
`Middle_name` , <br />
`Title` , <br />
`Position` , <br />
`Date_begin` ,<br />
`Date_end` , <br />
`Current_position` , <br />
`Links` , <br />
`Link_url_1` , <br />
`Link_name_1` , <br />
`Link_url_2` , <br />
`Link_name_2` ) <br />
VALUES ( <br />
'Mysinger', <br />
'Michael', <br />
'M', <br />
'Ph.D.', <br />
'Graduate Student', <br />
'2006', <br />
'2012', <br />
'Senior Scientist and Lead Developer', <br />
'1', <br />
'http://www.seachangepharma.com/', <br />
'SeaChange Pharmaceuticals', <br />
'', '' );<br />
Then to remove Michael from the people table (where the current lab members are listed): <br /><br />
update `webpage`.`people` set `active`= '0' where `Last_name`='Mysinger';<br />
<br />
= Updating when new staff joins =<br />
When a new person starts with the lab you need to add them to the people table: <br />
describe people;<br />
+-------------------+--------------+------+-----+---------+-------+<br />
| Field | Type | Null | Key | Default | Extra |<br />
+-------------------+--------------+------+-----+---------+-------+<br />
| first_name | varchar(100) | NO | | | |<br />
| middle_name | varchar(100) | YES | | | |<br />
| last_name | varchar(100) | NO | PRI | | |<br />
| e-mail | varchar(100) | NO | | | |<br />
| phd | tinyint(1) | YES | | 0 | |<br />
| position | varchar(100) | NO | | | |<br />
| Status | varchar(100) | NO | | | |<br />
| programme | varchar(100) | YES | | | |<br />
| link_to_programme | varchar(100) | YES | | | |<br />
| photo | varchar(100) | NO | | | |<br />
| project | text | YES | | NULL | |<br />
| active | tinyint(1) | NO | MUL | 1 | |<br />
+-------------------+--------------+------+-----+---------+-------+<br />
12 rows in set (0.00 sec)<br />
To add a new person you need their:<br />
First name<br />
Last name<br />
email<br />
phd =1 if they have their phd<br />
position (ie Postdoc, Graduate Student, etc) <br />
Status =’M’ always, I have no idea why<br />
photo= When you get a lab member’s photo, move it to the following directory: <br />
/domains/www.bkslab.org/htdocs/photos/lab_members<br />
and you have to name it: name_li.jpg<br />
So say the person’s name is Ann Fann name the image afann_li.jpg<br />
Again, I don’t know why.<br />
active = 1<br />
== Example when staff joins ==<br />
Here is an example:<br />
INSERT INTO `webpage`.`people` (<br />
`first_name` ,<br />
`middle_name` ,<br />
`last_name` ,<br />
`e-mail` ,<br />
`phd` ,<br />
`position` ,<br />
`Status` ,<br />
`programme` ,<br />
`link_to_programme` ,<br />
`photo` ,<br />
`project` ,<br />
`active`<br />
)<br />
VALUES (<br />
'Dah', '', 'Duan', 'mikeduan@gmail.com', '1', 'Postdoc', 'M', '', '', 'The formation of soluble colloids(aggregates) by small organic molecules including well-known drugs is a phenomenon discovered in the Shoichet lab more <br /> than a decade ago. Although some physical characteristics of these colloids have been investigated, the biophysical basis of this phenomenon is largely unknown. A primary goal of my research is to understand the mechanism <br /> of colloid formation at the atomic level. A second area of my researches focuses upon the idea of whether there is a relationship between drug colloids and their pharmacokinetics in vivo. A third area of interest is <br /> the utilization of colloidal drug formulations to enhance specificity and efficacy of drug delivery.', NULL , '1'<br />
);<br />
<br />
=Updating Publications=<br />
TO ADD A PUBLICATION:<br />
describe publications;<br />
+-------------------------+---------------------------------+------+-----+---------+-------+<br />
| Field | Type | Null | Key | Default | Extra |<br />
+-------------------------+---------------------------------+------+-----+---------+-------+<br />
| Id | int(11) | NO | | 0 | |<br />
| Authors | varchar(255) | NO | | | |<br />
| Title | varchar(255) | NO | | | |<br />
| Journal | varchar(100) | NO | | | |<br />
| Volume | varchar(10) | NO | | | |<br />
| Editor | varchar(100) | NO | | | |<br />
| Issue | varchar(10) | NO | | | |<br />
| Pages | varchar(10) | NO | | | |<br />
| Year | int(4) | NO | | 0 | |<br />
| Publisher | varchar(100) | NO | | | |<br />
| City | varchar(100) | NO | | | |<br />
| Type | set('paper','review','chapter') | NO | | paper | |<br />
| Pub_med_link | mediumtext | NO | | NULL | |<br />
| Doi_link | mediumtext | NO | | NULL | |<br />
| Number_additional_links | int(11) | NO | | 0 | |<br />
| Additional_link_1_url | mediumtext | NO | | NULL | |<br />
| Additional_link_1_txt | varchar(100) | NO | | | |<br />
| Additional_link_2_url | mediumtext | NO | | NULL | |<br />
| Additional_link_2_txt | varchar(100) | NO | | | |<br />
| Additional_link_3_url | mediumtext | NO | | NULL | |<br />
| Additional_link_3_txt | varchar(100) | NO | | | |<br />
| Additional_link_4_url | mediumtext | NO | | NULL | |<br />
| Additional_link_4_txt | varchar(100) | NO | | | |<br />
| Additional_link_5_url | mediumtext | NO | | NULL | |<br />
| Additional_link_5_txt | varchar(100) | NO | | | |<br />
| Additional_link_6_url | mediumtext | NO | | NULL | |<br />
| Additional_link_6_txt | varchar(100) | NO | | | |<br />
| Additional_link_7_url | mediumtext | NO | | NULL | |<br />
| Additional_link_7_txt | varchar(100) | NO | | | |<br />
| Additional_link_8_url | varchar(100) | NO | | | |<br />
| Additional_link_8_txt | mediumtext | NO | | NULL | |<br />
| Additional_link_9_url | varchar(100) | YES | | NULL | |<br />
| Additional_link_9_txt | varchar(100) | YES | | NULL | |<br />
| Picture | varchar(100) | NO | | | |<br />
| Group | varchar(10) | NO | | | |<br />
+-------------------------+---------------------------------+------+-----+---------+-------+<br />
35 rows in set (0.00 sec)<br />
<br />
To get the next Id, see what the last one was by typing:<br />
SELECT Id FROM publications ORDER BY Id<br />
Or the easiest way:<br />
SELECT MAX(Id) FROM webpage.publications;<br />
Then say the max entry was 124, you would use 125.<br />
<br />
To see most current publications of the lab go to:<br />
http://www.ncbi.nlm.nih.gov/pubmed/?term=Shoichet+BK<br />
<br />
<br />
==Example of publication update==<br />
Here is an example of a publication: http://www.ncbi.nlm.nih.gov/pubmed/23896298<br />
<br />
J Mol Biol. 2013 Nov 15;425(22):4569-83. doi: 10.1016/j.jmb.2013.07.030. Epub 2013 Jul 26.<br />
Blind prediction of charged ligand binding affinities in a model binding site.<br />
Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA.<br />
<br />
For this example, the following is what the different columns should have:<br />
Journal = J Mol Biol<br />
Year = 2013<br />
Volume = 425<br />
Issue = 22<br />
Pages = 4569-83<br />
Title = Blind prediction of charged ligand binding affinities in a model binding site. → Make sure you leave out the period at the end<br />
Authors = Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA<br />
Pub med link = http://www.ncbi.nlm.nih.gov/pubmed/23896298 ---> Make sure you leave out the “http://” part<br />
Doi link = dx.doi.org/10.1016/j.jmb.2013.07.030.x</div>Benrwong