PiMS 2.2General Description

Anne PajonEMBO Workshop September 2008

Tutorial this afternoon…

■ PiMS home page [Anne]■ Create Targets [Peter]■ Create Constructs [Chris]■ Sample Management [Bill]■ Protocol Editor [Ed]■ Experiments [Chris]■ Plate Experiments [Ed]■ Working on complexes [Peter]■ Recipes [Bill]

Simple key concepts

Can be linked together to model complex workflows■ Targets

■ Description of sequences, store annotations ■ Constructs

■ Starting points for real experiments, link to targets

■ Samples ■ Tracked samples made & used by experiments■ Samples have types, owners, locations etc.

■ Protocols■ Template for experiments

■ Single & plate Experiments■ Take one (or more) sample(s), produce new

sample(s) as outputs

Target

■ Two alternative methods to record them■ 'Manual’

■ By entering the Target details into a form ■ 'Automatic'

■ By entering an identifier or accession number and downloading the details from a remote database - such as SwissProt or GenBank

■ Targets recorded into PiMS can be linked to form a complex

Construct

■ Linked to Target record and stored as a 'Construct design' experiment

■ Information recorded■ Forward and Reverse Primers■ Three sample records: forward primer, reverse

primer and template■ Calculated values: Tm and % GC for the

primers, and the length, pI and Extinction coefficient for the expressed and final protein sequences

■ Three methods for recording the details of a construct■ User-defined primer length■ User-provided primer sequence■ User-defined Tm

Sample & Recipe

■ Physical sample ■ e.g. a volume of liquid in a container■ Inputs and outputs of an experiment, or

aliquots of reagents

■ Recipe of stock solutions ■ Three choices for how you record reagents

■ Text field in protocol e.g. when always same reagent■ Create a stock solution from a Recipe e.g. when use

different types of a particular reagent (different antibiotics)

■ Create a stock solution from a Recipe, track batch numbers or shelf life by recording each time they are used e.g. mixing stock solutions

Protocol

A protocol is a reusable user-defined template describing what you record for your experiments ■Set Up Parameters

■ E.g. incubation temperature or the number of PCR cycles; promoter sequence; was reagent added?

■Input Samples■ Samples or reagents used when performing an

experiment that you wish to track, e.g. primers, host strains

■Output Samples■ Samples or reagents produced when

performing an experiment that you wish to track

Experiment

■ Use a protocol to define the information needed to be recorded■ Parameters ■ Input & output samples■ Associate files (images and data)

■ Output samples of previous experiment are mapped to input samples of next (Provided sample type matches!)

■ User interface for plate experiments gives graphical and spreadsheet views■ Allows editing, reformatting and spreadsheet

upload

Type of PiMS items

■ Typing helps PiMS offer sensible choices■ only a plasmid can be used for transfection

experiments…

■ Samples■ Typed to show what they are ■ Input/Output samples for protocols

■ State what type of sample can be used and what is produced

■ Experiments and protocols ■ An experiment type is defined by its protocol.

A protocol type links similar protocols together