A Standard Operating Procedure for Systems Biology should adress at least the following items:            
  1 Study object  
  2 Study design  
  3 Experimental conditions  
  4 Parameters to be measured  
  5 Measuring methodologies  
  6 Assay and model validation  
  7 Modeling software  
  8 Record keeping, data collection/storage/access  
  9 Reporting and publishing  
  10 Project management                    
The following shows when and how often these were presented and discussed at the standards workshop.
Workshop G/H on Standards in Systems Biology at ICSB 2004 in Heidelberg on 10/10/04              
Speaker Subject Adressed in SOP item #    
Carsten Kettner Experimental conditions             3      
on Strenda Parameters under study 4  
  Database characteristics 7 and 8  
  Reporting methods 9  
Discussion --------------- How can we agree to agree 1 thru 10  
  Study same cells or organism 1  
  Use of model templates 7, 8, 9  
  Unified methodology 5, 6, 7  
  Intracellular conditions 1, 3, 4  
    Reconsider past results             Not adressed    
Dietmar Schomburg  High-quality database and thesaurus     5, 6, 7, 8, 9  
on Brenda Chaotic data 2, 3, 4, 5  
  Source and history of cells 1  
Discussion --------------- Atom-mapping info 3, 4, 5  
  Thermodynamics info 3, 4, 5  
  Enzyme units 3, 4, 5  
  Protocols, reporting 8, 9  
  Referee quality 9  
  Range of experimental conditions  3  
    Value of in vivo comparisons             2, 6      
Uwe Sauer Data authentication 8  
on measuring flux Assay validation and diversification 6  
  No single method sufficient Not adressed  
  Highest quality not always needed 2, 5, 6  
  Data inconsistencies become visible 8, 9  
  Start with "low quality" 2, 5, 6  
YSBN Strains and conditions 1, 3  
  Raw data 8  
  Simple physiology 2, 3, 4  
  Data clustering 6, 7  
Discussion --------------- Include genome info 1, 4  
  Include flux data 4  
  Try "grading" data quality 5, 6  
  Data variability and statistics 2, 5, 6, 8  
  Reporting and publishing standards 9  
    Protocol disambiguation             2      
Jildau Bouwman Try aligning labs and study objects     1, 2, 3, 4, 5  
on standardization Allow for serendipity Not adressed  
  Use "right" sampling frequency 3  
  Define experimental conditions 3, 5, 6, 7  
Discussion Sampling frequency 3  
  Selection of strains 1  
  Keep strain number minimal 1  
  Use timetable when switching strains 1  
  Polymorphism in strain sequence 1  
    Incorporate other disciplines' databases           8      
Workshop G/H on Standards in Systems Biology at ICSB 2004 in Heidelberg on 10/10/04              
Speaker Subject Adressed in SOP item #    
Jan-Marie Francois Arrest all metabolic activity             3      
on standardization  Standardize extraction methods 3, 4  
of metabolic  Standardize assay methods 5, 6  
sampling Result dependent on method 5, 6, 7  
  Avoid cell lysis 3, 4, 5, 6  
  Common method unlikely to evolve 2, 3, 4, 5, 6, 7  
  Differentiate between free and bound metabolites 4  
Discussion --------------- Add non-invasive methods 5  
  Metabolite compartmentalization 3, 4, 5, 6  
    Use more than one method             5      
Ursula Klingmueller Cell proliferation and differentiation     3, 4  
on SB standards Traditional methods insufficient 4, 5, 6  
  Mathematical modelling approach 6, 7  
  Resolution in time and space needed 4, 5  
  Biologists need "reward"  9, 10  
  Describe dynamic behavior 4  
  Strict SOP's needed 1 thru 10  
  Multidisciplinary approach needed 4, 5  
  Aim for highest data quality 2, 5, 6  
  Stimulate comm. between modellers and experimenters 10  
Discussion --------------- Make new start involving all relevant disciplines 10  
  Take the EU-wide perspective 1 thru 10  
  Compare "biological" errors to "technological" errors 5,6  
  Re-appraisal of "old" data needed Not adressed  
  What about "industrial reality"? 10  
  Even data of imperfect quality can make models work 5, 6, 7  
    Don't tell biologists about their need for reward         9, 10      
Ursula Kummer Facilitate IT-access for non-nerds      7, 8, 9, 10  
on Interfacing users Standardize computational methods 6, 7  
with modelling Sticking to GUI standards often suffices for publication 6, 7, 9  
  Use automation maximally, mathematics minimally 5, 6, 7  
  Selection of methods should be rational 3, 4, 5  
  Use web-based databases to facilitate modelling 8  
Discussion --------------- Streamline issues by using SBML and GUI interface 6, 7  
  Use models that can be understood and interpreted 6  
  Set required level of mathematics as low as possible 6, 7  
  Improve model reproducibility 6, 7  
  Use clearly identifiable algorithms and software 7  
  Create non-profit source of available software 7  
    Stick to agreed nomenclature             6, 7, 9      
Andrew Finney Use open-access, accepted standard     6, 7  
on SBML SBML supported by over 60 software applications 7  
  SBML stimulates collaboration between groups 10  
  Publication apportunities increased by using SBML 7, 9  
  SBML is extremely flexible 7  
  On-line validation possible 6  
Discussion --------------- Acronym usage questionable, thesaurus needed 7, 9  
  Introduce annotations in SBML 7  
  Terminology still cloudy 7, 9  
  Use SBML for stochastic models 6, 7  
  Simulation not dependent on SBML 6, 7  
  Available software has unspecified limitations 6, 7  
    Divide test suites in segments             6, 7      
Workshop G/H on Standards in Systems Biology at ICSB 2004 in Heidelberg on 10/10/04              
Speaker   Subject                 Adressed in SOP item #    
Sef Heijnen on Network structure substantiation important       4, 5, 6    
modelling kinetics Interactions are often non-linear 6  
  Limited controllability of parameters 4  
  Establish in-vivo parameters as well 1, 2, 3, 4  
  Characterize steady-state conditions 3, 4  
  Perturbations generate new data 3, 4  
  Living systems never reveal all potential data 1 thru 5  
  Extrapolation from in-vitro to in-vivo is difficult 2 thru 5  
  No "Grand Theory" sought after 2  
  Standards for kinetic studies needed 2 thru 5  
  Present parameters in a normalized way 4, 5, 6, 8, 9  
  Modelling achievable but difficult 6, 7  
  Cell-cycle averaging is unavoidable 2, 3, 4  
  Data-driven or model-driven? 2  
Discussion --------------- Selection of dynamic state conditions 2, 3, 4  
  Moving away from approximation causes trouble 5, 6  
  Approximations include linearizations 5, 6  
  New parameter-fitting could help SB 6, 7  
  Don't forget physiology 2, 6  
    Do cultures really exhibit steady-state conditions?         2, 3, 4      
Edda Klipp on  Publications are crucial for replicating experiments       2 thru 5, 9  
YSBN modelling Difference between prototype and reality 6, 7  
standards Compatibility issues 1 thru 9  
  Parameter change outcome should be realistic 4  
Discussion --------------- Publications often incomplete, template needed 9  
  Make all data available on the Web 9  
  Specify/explain use of symbols/acronyms 9  
  Clarify use of approximations 6, 7, 8  
  Provide access to software 7  
    Justify choice of similation parameters           6, 7      
Jacky Snoep on Behavior is a function of the components       4, 6, 7    
the Silicon Cell Measure parameters experimentally, in vivo too 4, 5, 6  
  Unify model storage in database 8  
  Integrate various model subsets 6  
  Apply rigorous model validation 6  
  Detail kinetics of all reaction steps 4  
Discussion --------------- Whole-cell perturbation important tool 4  
  Handle signal transduction data mathematically 6  
  Include and link various abstraction levels 6  
    Agree on merging modules into models           6      
The following table shows the relative frequency of each of the items adressed during the workshop
       SOP Items         No of times mentioned   Order of perceived importance    
1 Study object 16   item 6 most frequently mentioned  
2 Study design 23   items 4 and 7  
3 Experimental conditions 32   items 4 and 7  
4 Parameters to be measured 42   item 5  
5 Measuring methodologies 38   item 3  
6 Assay and model validation 49   item 2  
7 Modeling software 42   item 9  
8 Record keeping, data coll/stor/acc 15   item 1  
9 Reporting and publishing 17   item 8  
10 Project management         10       item 10 least frequently mentioned  
A more detailed description of the SOP items is given below
1 Study object         a. Type of cell or tissue            
  b. Source, history, description of cells  
  c. Genome sequence  
  d. Storage of stock cultures  
            e. Cultures freely available        
2 Study design a. Exhaustive protocol    
  b. Commonly available standards/controls  
  c. Appropriate statistics  
            d. Regular SOP review and authorization        
3 Experimental conditions     a. Culture medium/preparation/supplier  
  b. Culture medium refresh rate/method  
  c. Culture medium pH regulation  
  d. Culture vessel characteristics (roller bottle, spinner flask, fermentor)  
  e. Oxygen supply rate/method  
  f. Temperature regulation  
  g. Waste removal rate/method  
  h. Cells as monolayer, in suspension, on carrier  
  i. Shaking or stirring rate/method    
  j. Sampling rate/method  
  k. Sample identification/storage   
            l. Perturbation rate/method        
4 Parameters to be measured   a. Metabolic indicators    
  b. Enzyme activity/specificity  
  c. Concentration/structure/size/folding of intracellular molecules  
  d. Flux of carbon/nitrogen/ions  
  e. Cell density, size, shape, motion, doubling time  
  f. Spatial organization of cell components  
  g. Vesicle/follicle formation  
  h. Thermodynamics  
  i. Membrane permeability/fluidity/elasticity  
  j. Secretory activity  
  k. Electrical activity  
  l. Genome expression  
  m. Atom mapping  
            n. Force-fields              
5 Measuring technologies     a. Mass (concentration/flux)  
  b. Structure (sequence/folding/shape)  
  c. Size (Mol.Wt./Angstrom)   
  d. Motion (cilia/flagella/axon)  
  e. Enzyme (specificity/activity)  
  f. Electrical phenomena (charge, potential, polarity)  
            g. Optical properties            
6 Assay and model validation   a. Independent confirmation/validation of assays  
  b. Assays to be specific, precise, accurate, reproducible  
  c. Iterative confirmation/modification/validation of models  
  d. Use models that can be understood and interpreted  
            e. Compare model outcome to in vivo realities       
7 Modeling software   a. Software published and freely available  
  b. Standardize computation methods  
            c. Guarantee reviewers' access to modeling software      
8 Record keeping, data coll/storage/access     a. Lab notebooks to be dated, authenticated, signed and countersigned  
  b. Source and shelf-life of all experimental compounds fully documented  
  c. Electronic copy of records maintained locally and centrally  
  d. Unified storage method of models in database  
            e. Freele accessible web-based databases        
9 Reporting/publishing   a. Electronic template for protocols, reports and articles  
  c. Web-based European Journal of Systems Biology  
  d. Images, graphs tables and legends to be included in full-text searches  
  e. Selection procedure for referees formalized  
            f. Printed abstracts available for public understanding, press and media  
10 Project management   a. Full description of objectives, timelines, deliverables, owners, substitutes   
  b. Regular team meetings scheduled  
            c. Acknowledgement of funding and potential competing financial interest