1. PiMS 2.2 General Description Anne Pajon EMBO Workshop September 2008

2. 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]

6. 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

7. 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

9. 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

11. 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

13. 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

15. 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

19. 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