[BBF Standards] Two separate standards
Deepak Chandran
deepakc at u.washington.edu
Sun Mar 16 19:03:21 EDT 2008
Raik,
You can ease the question #2 from my last e-mail. I think you had
already answered that in your last e-mail (apologies).
--Deepak
Deepak Chandran wrote:
> Hello Raik,
>
> Thank you for the elaborate reply. I am afraid I am still not clear on a
> few things. I am sorry for continue this discussion for so long, but I
> am hoping it will be fruitful in the end. I think the following two
> questions should resolve my confusions:
>
> 1) Can you give an example of a composite part (single DNA strand with
> multiple parts) that can be fully described without any kind of
> descriptions on how the individual parts influence one another (i.e.
> "circuit diagram")? Additionally, can you give an example where the
> sequence is necessary to describe the composite part (assuming that the
> individual parts have not been altered in any way), except for spacers?
>
> 2) Suppose I make an oscillator using available parts. The oscillator is
> contained on a single plasmid. It does not really have any defined
> input/output -- it just expresses three repressors that oscillate.
> Small question: is this a still device, even though it cannot be
> connected to anything else?
> Bigger question: suppose I want to replace one of the repressors inside
> the part. Would I need to get the sequence of the part, identify the
> original repressor sequence, and then cut/paste the new repressor
> sequence? This would be "hacking" and not quite "engineering".
>
> --Deepak
>
> Raik Gruenberg wrote:
>
>> Hi Deepak,
>>
>> Deepak Chandran wrote:
>>
>>> Hello Raik and rest,
>>>
>>> Reshma's description on devices is very clear (on the link you had
>>> provided). My discussions were targeting basic biological parts vs
>>> composite parts (instead of basic parts vs devices). Turning a part
>>> into a device is a matter of adding the correct interface and
>>> identifying the function (correct?).
>>>
>> Half-correct. The difference is also that a device can (and often
>> will) bundle disconnected parts into a single functional unit. With
>> disconnected I mean parts that are *not* linked up into a single
>> composite Biobrick but are, for example, co-transfected on different
>> plasmids but need to *work* together (rather than being coded
>> together). The classic example are the quorum sensing devices. There
>> is a receiver and a sender but the receiver is in one strain and the
>> sender in another. It's sensible to unite them into one device because
>> they operate together and the PoPS interface is defined like cell1 ->
>> sender [black box] receiver -> cell2. But no single (composite or not)
>> part can implement this device. Many other devices *can* be
>> implemented in a single composite part, as a matter of convenience,
>> don't have to. I think that devices that are distributed within or
>> across cells may actually become the normal case in the future.
>>
>>
>>> Nonetheless, any composite part is a circuit made from basic parts. This
>>>
>> Here I disagree. A composite part is simply a part that happens to be
>> composed of other parts. Full stop. No interfaces or circuit implied.
>> Just a technical feature of the assembly process. A matter of
>> technical convenience and choice.
>>
>>
>>> circuit wiring diagram is very important to include in our standard
>>> representation of any composite part, whether it is an complex
>>> oscillator or a protein generator. Such a circuit wiring diagram does
>>>
>> An oscillator is a device. In many (not all) cases, this device *can*
>> be implemented in a single composite biobrick but doesn't need to. If
>> the implementing engineer decides to bundle all parts of the
>> oscillator into a single composite part, then the resulting device
>> "coincides" with this single composite part. But that's a technical
>> choice.
>>
>>
>>> not exist for basic biological parts (correct?).
>>>
>>> This does not have anything to do with the Registry's hierarchy or
>>> what family a part belongs under. I am just saying that in order to
>>> fully describe a composite part, I would need different descriptors
>>> than when describing a basic part.
>>>
>> So I would then argue that you are still talking about the description
>> of devices. You would create a composite Biobrick and then you wrap
>> this composite Biobrick into a device to describe its interfaces and
>> operation characteristics. Even better, you as designer describe the
>> device in detail including the full parts-list and all connections,
>> and the implementing engineer can from this blueprint decide whether
>> all parts need to be next to each other on a single piece of DNA or
>> whether he prefers to break the device into several co-expressed
>> parts. This also means that a given device will, in contrast to a
>> Biobrick part, not any longer correspond to an exact DNA sequence, at
>> least not a single consecutive DNA sequence.
>>
>>
>>> Additionally, I do not understand why the sequence information is
>>> needed for composite parts -- isn't this redundant information which
>>> makes room for errors in a database?
>>>
>> Sorry, I put that wrong. The definition on the standards wiki is
>> clearer. Composite Biobricks are defined as a "sequence" of basic
>> biobricks plus the intervening scar. So there is no redundancy. This
>> is also how I implemented it in the Brickit data scheme. The point was
>> that a composite Biobrick still has a unique DNA sequence (which can
>> be calculated from the sub-part sequences).
>>
>>
>>> If there are two representations (for basic and composite parts), the
>>> I agree with Ralf that they should not be allowed to wander
>>> completely independent of one another.
>>>
>> There should be a clear distinction between devices and parts
>> (=Biobricks for our task) but composite and basic parts are just two
>> variants of the same thing. This also allows us to first nail down the
>> "minimal" data exchange standard for Biobricks (composite and basic)
>> which will foremost cater to the search, assembly and exchange of
>> Biobrick DNA fragments. In parallel we (or you and Ralfph :-) can
>> start working on the description of devices. The minimal Biobrick
>> standard may already include the concept of a "Biobrick Device" as a
>> bag of Biobricks working together but without much further details.
>>
>> Well, there remain interesting questions how to distribute functional
>> descriptions between devices and parts. Should a Ribosomal Binding
>> Site part be also wrapped into a device (Input interface:
>> Ribosome-affinity, output interface: PoPS)? I was hoping to solve this
>> with the Biobrick family concept.
>>
>> Greetings,
>> Raik
>>
>>
>>> --Deepak
>>>
>>> Raik Gruenberg wrote:
>>>
>>>> Hi Deepak,
>>>>
>>>> the starting point of your interesting discussion may be a mix-up of
>>>> the terms 'device' and 'part'. Which is kind of not surprising
>>>> because our use of the terms is often fuzzy. Please have a look at
>>>> our current Biobrick, Part, Device definition (and comment if there
>>>> is anything unclear or inconsistent):
>>>>
>>>> http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Exchange#What_is_a_Biobrick.3F
>>>>
>>>>
>>>> So parts/Biobricks are the physical pieces of DNA that are passed
>>>> around -- something you can put into a plasmid, run on a gel,
>>>> sequence, etc. Composite Biobricks are still the very same, their
>>>> sequence (which is still unique) just happens to be a concatenation
>>>> of other Biobricks.
>>>>
>>>> As Drew and Josh pointed out, there is no single 'atomic' detail
>>>> level in biology but modularity is emerging in hierarchical layers.
>>>> So what you would consider a basic part may be constructed as
>>>> composite part by somebody else.
>>>>
>>>> By contrast, our definition of a device better approaches what you
>>>> were talking about:
>>>>
>>>> * Devices are combinations of one or more parts that have a
>>>> human-defined function.
>>>> * Some devices can be encoded in a single stretch of DNA (a basic or
>>>> composite part), others encompass disconnected parts (e.g. encoded
>>>> in two different locations, possibly even cells).
>>>> * (suggestion Reshma) Devices expose specified interfaces for their
>>>> functional connection with other devices (example: PoPS)
>>>> * (suggestion Raik) A Biobrick device is defined by a unique
>>>> combination of unique Biobricks
>>>>
>>>> So this is the level where we can start to create 'black boxes' with
>>>> standardized interfaces.
>>>>
>>>> Following this definition I would re-formulate your question ;-) Do
>>>> we need two different standards -- one for parts, and one for devices?
>>>>
>>>> IMO, since we already have two different names for it, we can keep
>>>> them in the same standard. We just have to keep the standard *open*
>>>> for the definition of interfaces and functions at different levels
>>>> (of modularity).
>>>>
>>>> Greetings,
>>>> Raik
>>>>
>>>> Deepak Chandran wrote:
>>>>
>>>>> Hello Josh, Drew, and rest,
>>>>>
>>>>> While it seems logical to first have standard definitions for
>>>>> promoter, rbs, coding regions, terminators, etc. before working on
>>>>> standards for devices and systems, I think the two are somewhat
>>>>> independent. People have been building biological circuits
>>>>> successfully (iGEM students for example). What I am proposing is
>>>>> for some of us (myself included) to write out a format that can
>>>>> represent all of the iGEM projects. This format can allow others to
>>>>> take iGEM projects (and any other such projects) and connect them
>>>>> together to form larger circuits without having to understand the
>>>>> details of the project itself. All these circuits will be
>>>>> represented in the standard language so that one does not need to
>>>>> reconstruct an entire device to reuse it. I think this is very much
>>>>> possible while the standards on promoters/rbs/etc are still
>>>>> pending. It is also a bit easier maybe, because many concepts can
>>>>> be borrowed from engineering disciplines.
>>>>>
>>>>> --Deepak
>>>>>
>>>>> Josh Perfetto wrote:
>>>>>
>>>>>> I think you are making some very insightful remarks without
>>>>>> realizing it :)
>>>>>> The only way to engineer large-scale systems is by breaking the
>>>>>> system down
>>>>>> into modular units with well-defined interfaces, otherwise it just
>>>>>> gets too
>>>>>> complex. The circuit diagram analogy is perfect: inputs, black
>>>>>> boxes, and
>>>>>> outputs, and I think it is a reasonable representation at this
>>>>>> level. If we
>>>>>> are defining things at this level, and have well-defined
>>>>>> interfaces like
>>>>>> PoPs for inputs and outputs, then I agree with you that it is not
>>>>>> necessary
>>>>>> to specify the DNA sequence of the entire circuit, but rather just
>>>>>> define
>>>>>> the order of the black boxes, which can define their own DNA
>>>>>> sequences. You
>>>>>> can replace one black box of the circuit diagram with another and
>>>>>> predict
>>>>>> what will happen. Once we standardize how to specify devices at
>>>>>> this level,
>>>>>> including devices with multiple inputs, it will be very powerful.
>>>>>>
>>>>>> When we drill down into other levels, like the upstream and core
>>>>>> portions of
>>>>>> a promoter, obviously PoPs is a totally useless interface for
>>>>>> defining how
>>>>>> these parts fit together, and so a circuit diagram is not
>>>>>> appropriate for
>>>>>> specifying the workings of a promoter as you said. We need to
>>>>>> decide at
>>>>>> which levels standardization would be useful and how to define
>>>>>> interfaces
>>>>>> between parts at these useful levels. However I don't think it's
>>>>>> essential,
>>>>>> at this stage, to model the world. For example, if we want to
>>>>>> standardize
>>>>>> how to define promoter behavior, we can leave the internals of
>>>>>> promoter
>>>>>> working as a black art, or at least out of the scope of
>>>>>> standardized parts,
>>>>>> and only define the characteristics of the promoter at that level,
>>>>>> at least
>>>>>> for now.
>>>>>>
>>>>>> I have not been in this community very long and am unsure about
>>>>>> the exact
>>>>>> definition that others are attributing to the term "devices" (and
>>>>>> I think
>>>>>> this does vary a bit, perhaps because it is not yet standardized
>>>>>> :) ). But
>>>>>> I don't see any problem with defining devices formally in terms of
>>>>>> A) PoPS
>>>>>> in/out, and B) other modifiers like UV/LuxR. I think a key
>>>>>> question is how
>>>>>> much these other modifiers from B are standardized in their
>>>>>> definition vs.
>>>>>> how much this is an ad-hoc definition. I think it's probably best
>>>>>> to follow
>>>>>> the 80/20 rule and standardize the 20% of properties that have are
>>>>>> used 80%
>>>>>> of the time, like chemical concentration, where the chemical in
>>>>>> question is
>>>>>> defined by something like CAS registry number, while leaving the
>>>>>> other
>>>>>> specialized properties that some devices might measure, like
>>>>>> magnetic field
>>>>>> orientation, unstandardized.
>>>>>>
>>>>>> -Josh
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Deepak Chandran [mailto:deepakc at u.washington.edu] Sent:
>>>>>> Friday, March 14, 2008 7:24 PM
>>>>>> To: Josh Perfetto
>>>>>> Cc: 'Drew Endy'; standards at biobricks.org
>>>>>> Subject: Re: [BBF Standards] Two separate standards
>>>>>>
>>>>>> Hello Josh and Drew and rest,
>>>>>>
>>>>>> The Polkadots system is a great example. Basically what I am
>>>>>> saying is that the sequence doesn't need to be specified in order
>>>>>> to define the polkadots system. As long as I know the parts and
>>>>>> the order in which they are placed on the plasmid(s), I can
>>>>>> reconstruct the system. By "interaction between parts", what I
>>>>>> mean is that in order to understand how polkadots is working, I
>>>>>> need to see the circuit that is presented on the polkadots
>>>>>> website. It would be nice if the circuit diagram was our standard
>>>>>> representation, but that is not reasonable.
>>>>>>
>>>>>> I think an operon is a similar case -- it is a very simple
>>>>>> circuit. One can draw a diagram that explains how an operon
>>>>>> functions. So, I am looking at operons as engineered objects
>>>>>> (though humans didn't engineer them first).
>>>>>>
>>>>>> What I am proposing is that circuits such as polkadots or even
>>>>>> operons should be defined in such a way that a synthetic biologist
>>>>>> can cut out one of the components of the circuit and replace it
>>>>>> with another device/part. If we cannot do that, then these
>>>>>> biological circuits are not engineerable.
>>>>>>
>>>>>> On the contrary, a promoter is different. I don't know how one can
>>>>>> explain the inside of a promoter using a circuit diagram. The fact
>>>>>> that promoters can be broken down into smaller components is true.
>>>>>> But can you take the first half of one promoter and stick it to
>>>>>> the second half of another promoter (I don't know)? Would the
>>>>>> resulting promoter have predictable behavior? Similarly, can I
>>>>>> take pieces of two RBS and piece them together and be able to
>>>>>> predict the function of the resulting RBS? In constast, replacing
>>>>>> the promoter or RBS inside an operon has predictable behavior, and
>>>>>> the affect of replacing parts inside the polkadots can also be
>>>>>> predicted (just like I can predict the result of changing my
>>>>>> computer's CPU). I suppose one could say replacing protein domains
>>>>>> has predicable behavior.
>>>>>>
>>>>>> By "interaction between parts", I did not mean any particular type
>>>>>> of interaction. But I was not clear on this: is PoPS the standard
>>>>>> input/output for BioBrick parts? Does this mean that I cannot have
>>>>>> a device that uses UV as an input and/or produces LuxR as an output?
>>>>>>
>>>>>> --Deepak
>>>>>>
>>>>>> Drew Endy wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Not true. A promoter can be disassembled, for example in
>>>>>>> bacteria, into -10 and -35 regions.
>>>>>>>
>>>>>>> You may find it helpful to stop thinking about natural objects
>>>>>>> such as operons and start thinking about devices as *engineered*
>>>>>>> objects.
>>>>>>>
>>>>>>> For example, consider the material produced in 2004 by the
>>>>>>> Polkadorks:
>>>>>>>
>>>>>>> http://parts.mit.edu/wiki/index.php/IAP2004:Polkadorks
>>>>>>>
>>>>>>> In the Polkadorks work you can see that they clearly defined
>>>>>>> device boundaries based on PoPS, including PoPS pass-through
>>>>>>> boundaries leading to multi-device mRNA.
>>>>>>>
>>>>>> Josh Perfetto wrote:
>>>>>>
>>>>>>
>>>>>>> Hi Deepak,
>>>>>>>
>>>>>>> I think that the view that a promoter cannot be sub-divided
>>>>>>> reflects a
>>>>>>> particular level of interest. From another point of interest, it
>>>>>>> would be
>>>>>>> very interesting to break promoters down into UPE, spacers, core
>>>>>>>
>>>>>>>
>>>>>> promoters,
>>>>>>
>>>>>>
>>>>>>> boxes, etc., and look at the "interactions within the part" with
>>>>>>> factors
>>>>>>> like UBF1.
>>>>>>>
>>>>>>> You are bringing up an interesting point with your operon. There
>>>>>>> are a
>>>>>>> couple ways you could define an operon. For example, you could
>>>>>>> create an
>>>>>>> operon sensitive to a specific repressor, and define it in part by a
>>>>>>> function that relates the concentration of that repressor to the
>>>>>>> level of
>>>>>>> polymerase that will flow out. Or, you could define it in such a
>>>>>>> way as
>>>>>>>
>>>>>>>
>>>>>> it
>>>>>>
>>>>>>
>>>>>>> has an interchangeable repressor sub-part, and define the operon
>>>>>>> in part
>>>>>>>
>>>>>>>
>>>>>> by
>>>>>>
>>>>>>
>>>>>>> a function which is dependent on another function defined by the
>>>>>>> sub-part
>>>>>>> part definition.
>>>>>>>
>>>>>>> If we were to take the first approach, it doesn't mean that the
>>>>>>> operon
>>>>>>>
>>>>>>>
>>>>>> can't
>>>>>>
>>>>>>
>>>>>>> be decomposed which obviously it can, it just means that such
>>>>>>>
>>>>>>>
>>>>>> decomposition
>>>>>>
>>>>>>
>>>>>>> is not an interface of the part, but an internal detail of the
>>>>>>> part. The
>>>>>>> second approach doesn't represent the ability to arbitrary
>>>>>>> combine parts
>>>>>>>
>>>>>>>
>>>>>> and
>>>>>>
>>>>>>
>>>>>>> be able to predict what will happen, but rather a part which is
>>>>>>>
>>>>>>>
>>>>>> specifically
>>>>>>
>>>>>>
>>>>>>> designed to take another part of a specific type and as a
>>>>>>> parameter and
>>>>>>> predict what will happen.
>>>>>>>
>>>>>>> But stepping back for a moment, aren't we now really discussing
>>>>>>> devices?
>>>>>>> I.e. the first approach is a single device with a PoPs out that's
>>>>>>>
>>>>>>>
>>>>>> dependent
>>>>>>
>>>>>>
>>>>>>> on a specific repressor, while the second approach is two
>>>>>>> devices, the
>>>>>>>
>>>>>>>
>>>>>> first
>>>>>>
>>>>>>
>>>>>>> with a PoPs out, and the second that relates its PoPs in and the
>>>>>>> level of
>>>>>>>
>>>>>>>
>>>>>> a
>>>>>>
>>>>>>
>>>>>>> specific repressor to produce a PoPs out value? When you say
>>>>>>> "the interaction between the parts is the crucial information",
>>>>>>> it seems that
>>>>>>> you're really either talking about an interface in terms of PoPs
>>>>>>> (in which
>>>>>>> case these parts could be called devices at least in my
>>>>>>> understanding of
>>>>>>>
>>>>>>>
>>>>>> how
>>>>>>
>>>>>>
>>>>>>> the term is being used), or are proposing that another interface
>>>>>>> besides
>>>>>>> PoPs be standardized in the definition of parts.
>>>>>>>
>>>>>>> -Josh
>>>>>>> -----Original Message-----
>>>>>>> From: standards-bounces at biobricks.org
>>>>>>> [mailto:standards-bounces at biobricks.org] On Behalf Of Deepak
>>>>>>> Chandran
>>>>>>> Sent: Friday, March 14, 2008 2:31 PM
>>>>>>> To: Drew Endy
>>>>>>> Cc: standards at biobricks.org
>>>>>>> Subject: Re: [BBF Standards] Two separate standards
>>>>>>>
>>>>>>> Drew,
>>>>>>>
>>>>>>> The parts,devices,systems hierarchy is fine. What is confusing to
>>>>>>> call an entire operon (possibly more than one promoter, rbs,
>>>>>>> gene) a "part" and a simple promoter a "part" as well. I can take
>>>>>>> an operon apart and replace one of the rbs, whereas the promoter
>>>>>>> cannot be taken apart. There is a difference between these two
>>>>>>> from an engineering perspective.
>>>>>>>
>>>>>>> I think that the operon should be defined in terms of the parts
>>>>>>> that it is made from and how they are interacting. Each
>>>>>>> individual part would then contain the sequence information and
>>>>>>> other characteristics. For anything made from multiple parts (say
>>>>>>> a bistable switch), the interaction between the parts is the
>>>>>>> crucial information. But if you take a basic part like a
>>>>>>> promoter, there is no interaction within the part. This is why I
>>>>>>> think that the standard definitions for basic parts and parts
>>>>>>> made from more than one part should be different.
>>>>>>>
>>>>>>> Again, I am completely open to disagreement here. It would be
>>>>>>> sufficient to explain how you can apply the same standards to
>>>>>>> describe a bistable switch and a promoter.
>>>>>>>
>>>>>>> --Deepak
>>>>>>>
>>>>>>> Drew Endy wrote:
>>>>>>>
>>>>>>>
>>>>>>>> Parts are parts. I'd use the language basic parts if you need a
>>>>>>>> modifier.
>>>>>>>>
>>>>>>>> Devices are composite parts. But, not all combinations of parts
>>>>>>>> are devices. Devices are limited by the requirements bounding
>>>>>>>> device specification. For example, polymerase per second (PoPS)
>>>>>>>> serves to define a common signal carrier for inputs and outputs
>>>>>>>> when dealing with gene expression devices.
>>>>>>>>
>>>>>>>> Note that there is no absolute physical definition of a part.
>>>>>>>> You can keep drilling down into particles and sub-atomics. So,
>>>>>>>> I believe that the standards should be linked to the
>>>>>>>> human-invented abstraction hierarchy (i.e., parts, devices,
>>>>>>>> systems), which was invented for practical reasons (i.e., it is
>>>>>>>> good for something). Support for reliable physical and
>>>>>>>> functional composition is definitely one of the first and best
>>>>>>>> goods that we can have.
>>>>>>>>
>>>>>>>> For the small amount of protein engineering work going on.
>>>>>>>> Docking and phosphorylation motifs are typically though of as
>>>>>>>> parts. For the small amount of RNA engineering work going on,
>>>>>>>> aptamers and ribozyme active sites are also thought of as parts.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mar 14, 2008, at 12:14 PM, Deepak Chandran wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hello standards group,
>>>>>>>>>
>>>>>>>>> From all the standards discussion, I think that there are two
>>>>>>>>> separate
>>>>>>>>> standards for parts. If this is the case, then it should be
>>>>>>>>> made explicit.
>>>>>>>>>
>>>>>>>>> The first type of standard is for atomic parts (better word
>>>>>>>>> needed?)
>>>>>>>>> such as promoters, rbs, etc. (that cannot be broken down
>>>>>>>>> further). The
>>>>>>>>> "standards" for these parts is simply a list of
>>>>>>>>> characteristics. For
>>>>>>>>> example, a promoter would have its sequence and Jason-units as its
>>>>>>>>> characteristic feature. RBS would have sequence and some other
>>>>>>>>> units.
>>>>>>>>> The list of characteristic features are probably best if
>>>>>>>>> developed by
>>>>>>>>> experimentalists -- the question to ask is: what is it that
>>>>>>>>> makes this
>>>>>>>>> promoter unique?
>>>>>>>>> Sequence information is definitely needed for atomic parts.
>>>>>>>>>
>>>>>>>>> The second type of standard is for composite parts (better
>>>>>>>>> word?) such
>>>>>>>>> as iGEM projects. I do not think that the sequence for
>>>>>>>>> composite parts
>>>>>>>>> is needed -- if we know the atomic parts that make up this
>>>>>>>>> composite
>>>>>>>>> part, then we can easily determine the sequence. What is needed
>>>>>>>>> is the
>>>>>>>>> order in which the atomic parts are arranged on the plasmid and
>>>>>>>>> the
>>>>>>>>> circuit-diagram that explains the mechanism of the part.
>>>>>>>>> Someone should
>>>>>>>>> be able to take a composite parts and replace some of the
>>>>>>>>> atomic parts
>>>>>>>>> just like upgrading a computer by replacing the RAM.
>>>>>>>>>
>>>>>>>>> One can wonder whether things like protein domains or fusion
>>>>>>>>> proteins
>>>>>>>>> are atomic or composites. I think the question is whether the
>>>>>>>>> part is
>>>>>>>>> modular (i.e. whether it can be taken apart and reconstructed
>>>>>>>>> using
>>>>>>>>> slightly different components).
>>>>>>>>>
>>>>>>>>> In summary:
>>>>>>>>> A language is needed for composite parts. (sequence not needed)
>>>>>>>>> A list of characteristics is needed for atomic parts. (sequence
>>>>>>>>> needed)
>>>>>>>>>
>>>>>>>>> If there is disagreement on this, please let me know why, so
>>>>>>>>> that I can
>>>>>>>>> eliminate my confusion. If there is agreement, then perhaps we
>>>>>>>>> should
>>>>>>>>> make this fact explicit and categorize our proposals to one of
>>>>>>>>> the two.
>>>>>>>>> We can make more directed progress that way.
>>>>>>>>>
>>>>>>>>> By the way, this categorization is not meant to disturb the
>>>>>>>>> part/device/system hierarchy.
>>>>>>>>>
>>>>>>>>> Ralf, I think that you language makes more sense if it is for
>>>>>>>>> composite
>>>>>>>>> parts, because you would need more descriptions for an atomic
>>>>>>>>> part. I
>>>>>>>>> will comment on that later.
>>>>>>>>>
>>>>>>>>> --Deepak
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Standards mailing list
>>>>>>>>> Standards at biobricks.org
>>>>>>>>> http://biobricks.org/mailman/listinfo/standards_biobricks.org
>>>>>>>>>
>>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Standards mailing list
>>>>>>> Standards at biobricks.org
>>>>>>> http://biobricks.org/mailman/listinfo/standards_biobricks.org
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> Standards mailing list
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>>>>>
>>>>>
>>>>>
>>>
>
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