Endy:Notebook/Synthetic Biology Open Language

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*'''[http://www.sys-bio.org/sbwWiki/doku.php?id=sysbio:contactus Herbert Sauro]''': Consider both logical and physical representations. This one looks closer to a physical representation. Do you have any plans for a logical representation? That is, a high level description that gives the logical design of the network with all the regulatory links and other notation required to describe its functional specification and one that could if required be converted into a mathematical representation (and a physical representation) suitable for analysis.  One could also imagine  higher level representations where a toggle switch, for example, might be represented as a single box rather than in terms of all its individual components.
*'''[http://www.sys-bio.org/sbwWiki/doku.php?id=sysbio:contactus Herbert Sauro]''': Consider both logical and physical representations. This one looks closer to a physical representation. Do you have any plans for a logical representation? That is, a high level description that gives the logical design of the network with all the regulatory links and other notation required to describe its functional specification and one that could if required be converted into a mathematical representation (and a physical representation) suitable for analysis.  One could also imagine  higher level representations where a toggle switch, for example, might be represented as a single box rather than in terms of all its individual components.
**'''[[Drew Endy|Drew]]''':Agreed that we want depictions across levels of abstraction.  To this end, please remember the Polkadorks ~2004:  http://parts.mit.edu/wiki/index.php/IAP2004:Polkadorks  Very simple device level diagrams, with solid PoPS wires, and dashed biochemical-specific wires:  http://parts.mit.edu/wiki/index.php/Image:Intro21-SystemDiagram.jpg  (Note also the green and red input and output tabs on the devices).  (We also had a representation of PoPS "pass-through" in which a PoPS input signal passes through a device, providing a matched output.  This was shown as a solid horizontal yellow bar, connecting input and output tabs.  At the next level down, see the "exploded" devices view, depicting functional parts:  http://parts.mit.edu/wiki/index.php/Image:Intro22-DeviceDiagram.jpg
**'''[[Drew Endy|Drew]]''':Agreed that we want depictions across levels of abstraction.  To this end, please remember the Polkadorks ~2004:  http://parts.mit.edu/wiki/index.php/IAP2004:Polkadorks  Very simple device level diagrams, with solid PoPS wires, and dashed biochemical-specific wires:  http://parts.mit.edu/wiki/index.php/Image:Intro21-SystemDiagram.jpg  (Note also the green and red input and output tabs on the devices).  (We also had a representation of PoPS "pass-through" in which a PoPS input signal passes through a device, providing a matched output.  This was shown as a solid horizontal yellow bar, connecting input and output tabs.  At the next level down, see the "exploded" devices view, depicting functional parts:  http://parts.mit.edu/wiki/index.php/Image:Intro22-DeviceDiagram.jpg
 +
*'''[[Barry Canton|Barry]]''': Big fan of a standard symbol set!  I would suggest that an effort be made to keep the icons as simple as possible (see [http://commons.wikimedia.org/wiki/File:Electrical_symbols_library.svg this] svg file of electrical symbols that are mostly just black lines as an example).  I think there are a couple of reasons to aim for simplicity -
 +
**If you encode meaning in color and complex graphical elements, the symbols become hard to approximate on a white board/sketch without loss of information.
 +
**Simple symbols won't go out of fashion as gradient fills, drop shadows and certain color-palettes may do in a few years.
 +
**The simpler the images, the more time you spend thinking about what they mean rather than about the images themselves (see [http://en.wikipedia.org/wiki/Chartjunk Chart Junk] for this idea applied to charts).
 +
**Easier to make, easier to edit, easier to support in software etc.
 +
**(Sorry for being old-fashioned).
== Design ==
== Design ==

Revision as of 11:20, 17 February 2009

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Project Description/Abstract

  • We are developing a "graphical" language for the formal description of BioBricks.
    • Truth be told, all languages are composed of visual symbols that are composed in space by a set of rules (syntax and grammar). Graphical languages are distinguished from textual languages only by the type of symbol. Textual languages use longstanding alphabets. Graphical languages use arbitrary symbols. In this instance, we are using arbitrary symbols to represent sequences of DNA that are part of a longer DNA sequence that has a known function. For example, a red pentagon represents a translational stop sequence in BioBrick vector pSB4K5-152002 (Shetty, 2008).
  • We aim to make the language an open standard.
    • Languages emerge from the friction of top-down control (eg. Preservation of the French Language) and bottom-up needs to communicate (eg. Pop Culture). With this in mind, we want the language to flourish in an environment of open communication while rigorously defining a finite set of symbols and grammar.
  • We are developing the language as an abstract tool for solving concrete problems.
    • Technical languages have an additional challenge of balancing the requirements of providing a philosophically consistent framework while still being useful for solving concrete problems. Balancing this tension is difficult and requires both top-down and bottom-up approaches. With that in mind, BOGL will have a rigorous and consistent structure and will be used in concrete software tools while working on concrete Synthetic Biology projects.

Review

Survey of Synthetic Biology Diagrams

Gallery

Other Graphical Notation Standards

Systems Biology Grahical Notation

Software Tools

Clotho - APE for BioBricks and more...

Tinkercell - A tool for biological network design and simulation; Sauro group

Literature

Use Cases

Coming soon...

Requirements

General

  • Provide a graphical notation that assists in making the description and development of BioBricks more time efficient.

Specific

  • Coming soon...

Discussion

  • Drew: Review and include the icons from the Registry
    • Cesar 15:36, 13 February 2009 (PST): I'm adding the Registry symbols ASAP.
    • Cesar 17:17, 15 February 2009 (PST): Done.
  • Reshma 08:20, 11 February 2009 (EST): The graphics might be more useful in a vector graphics format so that they scale nicely and can be used across presentations/publications/posters/wiki's etc. The Registry icons are not currently available as vector graphics; hence most folks are forced to make their own.
    • Cesar 12:50, 11 February 2009 (PST): Completely agree and will begin to convert the symbols to vector graphics. Everyone is welcome to help make the changes!
  • Reshma 08:20, 11 February 2009 (EST): Probably each icon should have a bar behind it as an iconic representation of the DNA. (See the Registry icons for an example.) The bar tends to be useful when depicting a sequence of parts.
    • Cesar 16:26, 15 February 2009 (PST): Completely agree. I will add this change to the new vector graphics-based symbols going up this week. The symbols on the Registry are an excellent starting point.
  • Reshma 08:20, 11 February 2009 (EST): It might make more sense to have icons that have identical widths and identical heights (though the width doesn't necessarily need to equal the height). I suspect that consistent heights and widths would make it easier to string together graphics automatically via computer programs.
  • Herbert Sauro: Consider both logical and physical representations. This one looks closer to a physical representation. Do you have any plans for a logical representation? That is, a high level description that gives the logical design of the network with all the regulatory links and other notation required to describe its functional specification and one that could if required be converted into a mathematical representation (and a physical representation) suitable for analysis. One could also imagine higher level representations where a toggle switch, for example, might be represented as a single box rather than in terms of all its individual components.
  • Barry: Big fan of a standard symbol set! I would suggest that an effort be made to keep the icons as simple as possible (see this svg file of electrical symbols that are mostly just black lines as an example). I think there are a couple of reasons to aim for simplicity -
    • If you encode meaning in color and complex graphical elements, the symbols become hard to approximate on a white board/sketch without loss of information.
    • Simple symbols won't go out of fashion as gradient fills, drop shadows and certain color-palettes may do in a few years.
    • The simpler the images, the more time you spend thinking about what they mean rather than about the images themselves (see Chart Junk for this idea applied to charts).
    • Easier to make, easier to edit, easier to support in software etc.
    • (Sorry for being old-fashioned).

Design

Symbols

Present Symbol Proposed Symbol Meaning
Image:Part_icon_terminator.png SVG Version Terminator
Image:Part_icon_signalling.png SVG Version Signal Sender/Receiver
Image:Part_icon_rna.png SVG Version RNA
Image:Part_icon_reporter.png SVG Version Reporter
Image:Part_icon_regulatory.png SVG Version Transcription Regulator
Image:Part_icon_rbs.png SVG Version Ribosome Binding Site
Image:Part_icon_measurement.png SVG Version Measurement Part
Image:Part_icon_inverter.png SVG Version Inverter
Image:Part_icon_generator.png SVG Version Protein Generator
Image:Part_icon_dna.png SVG Version DNA
Image:Part_icon_composite.png SVG Version Composite Part
Image:Part_icon_cds.png SVG Version Protein Coding
Image:Restriction_Site.png None Restriction Site
Image:Cloning_Site_Prefix.png None Cloning Site Prefix
Image:Cloning_Site_Suffix.png None Cloning Site Suffix
Image:Forward_Verification_Primer_Annealing_Site.png None Forward Verification Primer Annealing Site
Image:Reverse_Verification_Primer_Annealing_Site.png None Reverse Verification Primer Annealing Site
Image:Forward_Transcriptional_Terminator.png None Forward Transcriptional Terminator
Image:Reverse_Transcriptional_Terminator.png None Reverse Transcriptional Terminator
Image:Translational_Stop_Sequence.png None Translational Stop Sequence
Image:Replication_Origin.png None Replication Origin
Image:Open_Reading_Frame.png None Open Reading Frame
Image:Ampicillin_Resistance_Marker.png None Ampicillin Resistance Marker
Image:Chloramphenicol_Resistance_Marker.png None Chloramphenicol Resistance Marker
Image:Kanamycin_Resistance_Marker.png None Kanamycin Resistance Marker
Image:Tetracycline_Resistance_Marker.png None Tetracycline Resistance Marker

Grammar

Coming soon...

Formal Specification

Coming soon...

Implementation

  • Initial Set of Symbols
    • Released on 2-10-2009
    • Set of PNG images
    • This is a VERY rough draft meant for starting a conversation about a standard graphical notation.
    • Download

Maintenance

Coming soon...

Notes


Recent changes



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