This post is part of the second laboratory session!
We are going to start with a refresh of Bash command, and possibly learning some new one.
Perl & Genomics
Bioinformatics for Genomics Course – University of Padua
Category Archives: laboratory
First practical
Welcome to the first practical. During this practical you’ll learn how to master the command line and Linux as well.
Please, keep in mind that all the tools we are presenting day by day are necessary to fulfil the final assignment, so try to think about all the steps rather than rushing to the end.
Feel free to ask us, in case of troubles…
Last lab guys!
We are approaching the end of a cycle… during this genomics laboratory you put your hands on genome sequencing and finishing, and of course you had a nice «primer» on Perl programming, perhaps with a boost in your primer design skills as an extra bonus.
It’s time to sum up, with a «self service» laboratory…
Due to the remarkable success of this year laboratory, that has been an experiment I wanted to try, we will repeat the 20 hours “Perl practical” next year. So stay tuned 🙂
See you this afternoon,
Andrea
Refresh your Perl, the size you want.
Last laboratory: queries on a database
Welcome back guys!
Please, start reviewing what databases are so that we all have a common background when talking about tables and fields. Then we prepared a very short introduction to the SQL language:
These tasks are quite common, but not so useful to understand how databases works so we’ll just have a look to them.
Today you’ll play with the Linux machine with a good level of independence. Tomorrow we’ll use the CIV computer room where there is the possibility to use a projector for a more “guided” and commented experience. Consider this as tomorrow we will practice more with queries… while only today you’ll have the possibility to play with Perl if you wish to do so 🙂
MySQL: creating a new table
The very nice thing about MySQL is that… it’s very similar to fluent English. So if we want to create a table we must decide in advance the list of fields we need.
For each field we need to specify the type (will we store a number? a date? a name?). A list of fields types is available here.
Remember that MySQL is case-insensitive, while table names and field names are case-sensitive. It’s common to type SQL commands in upper case though, and to choose lowercase names. The “create table” command requires a name and a list of fields.
CREATE TABLE reagents ( id INT AUTO_INCREMENT PRIMARY KEY, name VARCHAR(100), supplier INT, amount INT, arrived DATE);
A single command ends with “;” in MySQL shell (this is not always true for SQL languages), so that we can split a single command across multiple lines. We choosed a list of fields and some of them store a number, another a date, the name is a string (varchar).
Each table has to have a “Primary Key“, a unique identifier for the record. A common practice is to use an integer with the “auto_increment” keyword that means: every time you create a record, the “id” field will be incremented.
If we later want to add a new field there’s a simple command to do this:
UPDATE reagents ADD (casnumber VARCHAR(20));
MySQL: first commands into the shell
MySQL has its own shell. We can enter using the following command:
mysql -h servername -u username -p
Where “servername” can be omitted if we installed MySQL in our computer. The prompt switches from “$” to “mysql>” and we can type SQL commands.
We want to:
- list the databases
- select a particular database
- list the tables in that database
- list the fields of a table
Databases: the very basic introduction
Databases… a whole ‘big thing’ in the bioinformatics field. Databases are the “backbone” of all the public data banks of course, but can be very useful for many other aspects. Even our scaffolding program uses a database for fast data retrieval.
Databases stores data, as a very simple “text file”. But they have a powerful engine to quickly retrieve data using selected criteria. Consider our “pick primer” program: it takes a while to take the sequence of both contigs because it has to parse the file containing all of them. If we decided to store all sequences into a database we could perform a simple query to get them.
This blog is powered by a quite complex database. Continue reading
Last soupper
Dear students,
we are approaching the end of this perlfect course… so we’d like to remind you about the two last practicals:
- 7th june – 2.30 pm, aula di bioinformatica via Paolotti
- 8th june – 2.30 pm, aula CIV, Vallisneri
Note that these dates are the correct ones, while we noted that the official Molecular Biology timetable seems to be wrong.
Attendance to these classes is not compulsory. People that decide to join us are requested to stay until the end of the practicals and to attend both.
Cheers,
Andrea and Elisa
PS: The test will cover some Perl basics, the general laboratory strategy (assembly, scaffolding, gap filling) and what you did in the wet lab. Don’t be afraid about Perl: the more you know the better it is but we don’t expect you to write a whole program from scratch. Reviewing past posts about our “pick primer” program is highly recommended though.
wet lab
Time to test experimentally your work on the computer!
Your primers were successfully ordered and will be delivered soon. As anticipated during the introduction to the laboratory, the primers will be resuspended in ultrapure water (to a concentration of 100µM) and diluted to obtain a working solution (concentration 10µM) using an automated system that makes the pipetting for us, as long as we pass to it the correct instructions.
As you experimented during the first part of this laboratory experience, being able to translate your practice into a list of actions to be carried out, makes you able to tell a computer to do something for you. You can also instruct the computer to drive a machine to carry out the work for you 😉
So only for this time we will let you run you PCRs by you selves.. next time you’ll be able to ask a robot to assembly them for you! Maybe I’m just joking.. but not that much.. find it out yourselves following this link.
Next week we will start with some practice about PCR and we will also produce our useful data to close a few gaps of the genome. Following this link (Wetlab protocol) you will find a copy of the laboratory protocol. Have a look at it. You will also find a copy on the lab bench, so no need to print it and bring it to the labs.
Instructions are really detailed even though many of you will have run a PCR before. Nevertheless there are a few advantages:
- provide you with enough instructions to be as more autonomous as possible
- use as much technical vocabulary as possible to help improve you english
- induce you to a correct lab practice