Lab Website: Difference between revisions

From DISI
Jump to navigation Jump to search
(Created page based on WWW & Wiki page from Lab Manual)
 
mNo edit summary
 
Line 220: Line 220:
  Pub med link = http://www.ncbi.nlm.nih.gov/pubmed/23896298  ---> Make sure you leave out the “http://” part
  Pub med link = http://www.ncbi.nlm.nih.gov/pubmed/23896298  ---> Make sure you leave out the “http://” part
  Doi link = dx.doi.org/10.1016/j.jmb.2013.07.030.x
  Doi link = dx.doi.org/10.1016/j.jmb.2013.07.030.x
[[Category::Sysadmin]]

Latest revision as of 21:42, 28 June 2016

THE LAB WEBSITE (www.bkslab.org)

MOVING THE LAB WEBSITE: On the

UPDATING THE LAB WEBSITE: 

Introduction

A little about the webpage database: As root:

mysql -p
use webpage
show tables;
+------------------------+
| Tables_in_webpage      |
+------------------------+
| Aggregators            |
| alumni                 |
| ampc_binders           |
| ampc_non_binders       |
| ccp_binders            |
| ccp_non_binders        |
| compounds              |
| l99a_binders           |
| l99a_m102q_binders     |
| l99a_m102q_non_binders |
| l99a_non_binders       |
| people                 |
| publications           |
+------------------------+
13 rows in set (0.00 sec)

Updating when staff leaves

I have only ever had to update alumni, people and publications: When some one leaves the lab you have to move them from the people table to the alumni table.

describe alumni;
+------------------+--------------+------+-----+---------+-------+
| Field            | Type         | Null | Key | Default | Extra |
+------------------+--------------+------+-----+---------+-------+
| Last_name        | varchar(100) | NO   |     |         |       |
| First_name       | varchar(100) | NO   |     |         |       |
| Middle_name      | varchar(100) | NO   |     |         |       |
| Title            | varchar(100) | NO   |     |         |       |
| Position         | varchar(100) | NO   |     |         |       |
| Date_begin       | int(11)      | NO   |     | 0       |       |
| Date_end         | int(11)      | NO   |     | 0       |       |
| Current_position | varchar(100) | NO   |     |         |       |
| Links            | varchar(100) | NO   |     |         |       |
| Link_url_1       | varchar(100) | NO   |     |         |       |
| Link_name_1      | varchar(100) | NO   |     |         |       |
| Link_url_2       | varchar(100) | NO   |     |         |       |
| Link_name_2      | varchar(100) | NO   |     |         |       |
+------------------+--------------+------+-----+---------+-------+
13 rows in set (0.00 sec)

Here is the steps to do that:

First, for the person that is leaving you need to have their:
First name
Last name
Title  =>  This is their title when they left the lab
Position => This is their title when they started at the lab
Date begin => date begin with lab
Date end  => date end with lab
Current position => Their title at their new job
URL links => Any url links they want associated with their name (and how they want them named).

Example when staff leaves

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:

INSERT INTO `webpage`.`alumni` ( 
`Last_name` , 
`First_name` , 
`Middle_name` , 
`Title` , 
`Position` , 
`Date_begin` ,
 `Date_end` , 
`Current_position` , 
`Links` , 
`Link_url_1` , 
`Link_name_1` , 
`Link_url_2` , 
`Link_name_2` ) 
VALUES ( 
'Mysinger', 
'Michael', 
'M', 
'Ph.D.', 
'Graduate Student', 
'2006', 
'2012', 
'Senior Scientist and Lead Developer', 
'1', 
'http://www.seachangepharma.com/', 
'SeaChange Pharmaceuticals', 
,  );

Then to remove Michael from the people table (where the current lab members are listed):

update `webpage`.`people` set `active`= '0'  where `Last_name`='Mysinger';

Updating when new staff joins

When a new person starts with the lab you need to add them to the people table:

describe people;
+-------------------+--------------+------+-----+---------+-------+
| Field             | Type         | Null | Key | Default | Extra |
+-------------------+--------------+------+-----+---------+-------+
| first_name        | varchar(100) | NO   |     |         |       |
| middle_name       | varchar(100) | YES  |     |         |       |
| last_name         | varchar(100) | NO   | PRI |         |       |
| e-mail            | varchar(100) | NO   |     |         |       |
| phd               | tinyint(1)   | YES  |     | 0       |       |
| position          | varchar(100) | NO   |     |         |       |
| Status            | varchar(100) | NO   |     |         |       |
| programme         | varchar(100) | YES  |     |         |       |
| link_to_programme | varchar(100) | YES  |     |         |       |
| photo             | varchar(100) | NO   |     |         |       |
| project           | text         | YES  |     | NULL    |       |
| active            | tinyint(1)   | NO   | MUL | 1       |       |
+-------------------+--------------+------+-----+---------+-------+
12 rows in set (0.00 sec)

To add a new person you need their:

First name
Last name
email
phd =1 if they have their phd
position (ie Postdoc, Graduate Student, etc)  
Status =’M’ always, I have no idea why
photo= When you get a lab member’s photo, move it to the following directory: 
           /domains/www.bkslab.org/htdocs/photos/lab_members
   and you have to name it: name_li.jpg
           So say the person’s name is Ann Fann name the image afann_li.jpg
   Again, I don’t know why.
active = 1

Example when staff joins

Here is an example:

 INSERT INTO `webpage`.`people` (
`first_name` ,
`middle_name` ,
`last_name` ,
`e-mail` ,
`phd` ,
`position` ,
`Status` ,
`programme` ,
`link_to_programme` ,
`photo` ,
`project` ,
`active`
)
VALUES (
'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 
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
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
the utilization of colloidal drug formulations to enhance specificity and efficacy of drug delivery.', NULL , '1'
);

Updating Publications

TO ADD A PUBLICATION:

describe publications;
+-------------------------+---------------------------------+------+-----+---------+-------+
| Field                   | Type                            | Null | Key | Default | Extra |
+-------------------------+---------------------------------+------+-----+---------+-------+
| Id                      | int(11)                         | NO   |     | 0       |       |
| Authors                 | varchar(255)                    | NO   |     |         |       |
| Title                   | varchar(255)                    | NO   |     |         |       |
| Journal                 | varchar(100)                    | NO   |     |         |       |
| Volume                  | varchar(10)                     | NO   |     |         |       |
| Editor                  | varchar(100)                    | NO   |     |         |       |
| Issue                   | varchar(10)                     | NO   |     |         |       |
| Pages                   | varchar(10)                     | NO   |     |         |       |
| Year                    | int(4)                          | NO   |     | 0       |       |
| Publisher               | varchar(100)                    | NO   |     |         |       |
| City                    | varchar(100)                    | NO   |     |         |       |
| Type                    | set('paper','review','chapter') | NO   |     | paper   |       |
| Pub_med_link            | mediumtext                      | NO   |     | NULL    |       |
| Doi_link                | mediumtext                      | NO   |     | NULL    |       |
| Number_additional_links | int(11)                         | NO   |     | 0       |       |
| Additional_link_1_url   | mediumtext                      | NO   |     | NULL    |       |
| Additional_link_1_txt   | varchar(100)                    | NO   |     |         |       |
| Additional_link_2_url   | mediumtext                      | NO   |     | NULL    |       |
| Additional_link_2_txt   | varchar(100)                    | NO   |     |         |       |
| Additional_link_3_url   | mediumtext                      | NO   |     | NULL    |       |
| Additional_link_3_txt   | varchar(100)                    | NO   |     |         |       |
| Additional_link_4_url   | mediumtext                      | NO   |     | NULL    |       |
| Additional_link_4_txt   | varchar(100)                    | NO   |     |         |       |
| Additional_link_5_url   | mediumtext                      | NO   |     | NULL    |       |
| Additional_link_5_txt   | varchar(100)                    | NO   |     |         |       |
| Additional_link_6_url   | mediumtext                      | NO   |     | NULL    |       |
| Additional_link_6_txt   | varchar(100)                    | NO   |     |         |       |
| Additional_link_7_url   | mediumtext                      | NO   |     | NULL    |       |
| Additional_link_7_txt   | varchar(100)                    | NO   |     |         |       |
| Additional_link_8_url   | varchar(100)                    | NO   |     |         |       |
| Additional_link_8_txt   | mediumtext                      | NO   |     | NULL    |       |
| Additional_link_9_url   | varchar(100)                    | YES  |     | NULL    |       |
| Additional_link_9_txt   | varchar(100)                    | YES  |     | NULL    |       |
| Picture                 | varchar(100)                    | NO   |     |         |       |
| Group                   | varchar(10)                     | NO   |     |         |       |
+-------------------------+---------------------------------+------+-----+---------+-------+
35 rows in set (0.00 sec)

To get the next Id, see what the last one was by typing:

SELECT Id FROM publications ORDER BY Id

Or the easiest way:

SELECT MAX(Id) FROM webpage.publications;

Then say the max entry was 124, you would use 125.

To see most current publications of the lab go to: http://www.ncbi.nlm.nih.gov/pubmed/?term=Shoichet+BK


Example of publication update

Here is an example of a publication: http://www.ncbi.nlm.nih.gov/pubmed/23896298

J Mol Biol. 2013 Nov 15;425(22):4569-83. doi: 10.1016/j.jmb.2013.07.030. Epub 2013 Jul 26. Blind prediction of charged ligand binding affinities in a model binding site. Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA.

For this example, the following is what the different columns should have:

Journal = J Mol Biol
Year = 2013
Volume = 425
Issue = 22
Pages = 4569-83
Title = Blind prediction of charged ligand binding affinities in a model binding site. → Make sure you leave out the period at the end
Authors = Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA
Pub med link = http://www.ncbi.nlm.nih.gov/pubmed/23896298   ---> Make sure you leave out the “http://” part
Doi link = dx.doi.org/10.1016/j.jmb.2013.07.030.x

[[Category::Sysadmin]]