pims 2.2 general description anne pajon embo workshop september 2008
TRANSCRIPT
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