Help:FAQ

Contents

We're developing our FAQ's section! If you have a question that isn't on this list, need further clarification, or have any comments, please contact iGEM HQ at hq (at) igem . org.


Getting started

How can I join iGEM and the Registry?

There are a several ways to get involved with our community!

If you'd like to...

  • take part in [http://2017.igem.org the iGEM competition], you will need to register as an iGEM Team.
  • sign up your academic lab, you can register for an iGEM Labs account
  • come to the [http://2017.igem.org/Giant_Jamboree 2017 Giant Jamboree], you can [http://2017.igem.org/Giant_Jamboree/Registration register to attend]
  • work for iGEM HQ, see our Jobs page, and contact us at jobs (at) igem . org
  • [http://2017.igem.org/Giant_Jamboree/Volunteers volunteer for iGEM and the Jamboree], contact us at hq (at) igem . org
  • sponsor iGEM and the Registry, contact us at hq (at) igem . org


What are the benefits of joining iGEM?


My team/lab has an iGEM account already, how can I join the group as member?

Once the PI has created a team/lab, they can give you a member activation code, or accept your pending membership into the iGEM team/lab account.

See the list of the iGEM 2017 Team or the list of iGEM labs.


I don't want to join an iGEM team/lab, can I purchase the distribution or parts instead?

iGEM does not sell the DNA Distribution or part samples.



Using Parts

How do I use the DNA Distribution?

The DNA Distribution contains over 1000 high-quality part samples as dried (miniprepped) DNA. Each sample is QC tested through sequencing and AB test plates.

While there is not enough DNA for assembly right out of the kit, you will be able to transform the DNA into competent cells and then make your own glycerol stocks of any part you wish. Please make sure to test the efficiency of your competent cells.

Please see the 2017 DNA Distribution help page for more information.


I've found a part I'd like to use. Does this part work as described?

Unfortunately, iGEM HQ cannot make any qualitative statements on if a part functions as described. However, part samples submitted to the Registry undergo quality control, including sequencing.

For functional characterization, we recommend taking a look at a part's main page and experience page for information on how the part works.


I've found a part I'd like to use. Does this part have a sample?

The Registry has thousands of documented parts, but not all of them have available samples. You can check the part's Status Box on the top right of a part's page.

Part's with an available sample, will say:

  • Sample in Stock
  • Sample it's Complicated


Do Registry parts only work in E. coli

While the Registry stores all of its part samples in E. coli (NEB 10-beta), we have many parts that are meant to be used in different organisms (chassis).

See the Registry catalog to find collections of parts organized by chassis.


Do I have to use 3A assembly to assemble parts?

Most of the parts in the Registry adhere to the BioBrick 10 RFC standard and most samples are in pSB1C3 a BioBrick plasmid backbone. As such, these samples can be assembled together using 3A Assembly, to create new parts that are both BioBrick compatible and in a BioBrick plasmid backbone.

Teams are allowed to assemble parts using any method they prefer: Type IIs enzyme methods (GoldenGate, MoClo, etc), Gibson, magnetic bead-based, or synthesis entirely. However, please remember that parts submitted to the Registry must be BioBrick compatible, and in pSB1C3.



Searching for Parts

How can I find parts on the Registry

You can enter a part name (BBa_) into the search bar above , or hover over the gray arrow for more search options.

The Registry has a variety of tools to let you search and browse parts. See the help pages on the Registry search tools and the catalog of parts and devices.


I'm looking for a part or device but I don't know the part name

You can browse the Catalog of Parts & Devices. The Catalog organizes the available parts of the Registry by various criteria. Please see the Catalog help page for more information.

Using the search drop down in the Registry menu, you can do a Google Site Search or Text Search. A Google Site Search or Text Search will let you search using a descriptor.


I know my part's name and want to go to its main page

If you know the part name (e.g., BBa_J04450), simply type the name (BBa_J04450, or J04450) into the search box at the top right corner of the Registry and hit enter. This immediately takes you to the Main Page for the part.


I want to find composite parts that contain my basic (or composite) part

You'll want to use the Find parts that use this part search option. This will list all the composite parts containing your part of interest. The parts that are available from the Registry will appear at the top of the search results. You can enter multiple parts, but they need to be in the correct order.


I'm putting together a composite part and would like to find any intermediate parts

You may find yourself putting together a composite part made of several basic parts. Before you begin assembling your part in the lab you'll want to use the Get help in assembling this part search option which will show you whether there are any parts in the Registry that match a portion of your composite part.


Can I search for parts by sequence?

The Registry currently does not have a dedicated search tool for searching for parts by sequence. However, you can use the Registry's Sequence Analysis tool to blast a sequence against all Registry parts. Or use the tools menu, and select DNA sequencing. The Sequence Analysis tool may take some time to load.


Can I browse through the DNA Distribution?

You can browse through the part samples in the Distribution Kit Plates or the entire Repository. In the Registry menu above, hover over the Repository menu, to see the Distribution or All Libraries

Please see the Browsing Distribution help page for more information



Quality Control

Where can I find the quality control information for a part sample?

The quality control information for a part sample is summarized on its Get This Part page. We recommend also taking a close look at the sequence results before using a part. You can do view the sample analysis page by clicking on the More... link next to a sample's sequence result.

Please see Quality Control for more information.


Do all part samples in the Registry have quality control information

The Registry does not have QC information for all of its part samples (particularly samples submitted before 2010). However since 2010, we have sequenced part submissions sent in pSB1C3.

Part's with an available sample that has been sequence confirmed or ends confirmed, will say:

  • Sample in Stock

You can see a summarized version of QC information on a part's Get This Part page.


How does the Registry sequence parts?

Parts are sequenced using the VF2(BBa_G00100) and VR (BBa_G00101) sites on the pSB1C3 (and other pSB_) plasmid backbone. Generally, parts that are under 1600bp are fully sequence confirmed.

However, long parts are not fully confirmed, and currently, the Registry does not do internal sequencing for these parts.


Are Confirmed parts guaranteed to work?

iGEM HQ cannot make any qualitative statements on if a part functions as described. For functional characterization, we recommend taking a look at a part's main page and experience page for information on how the part works.

Furthermore, we recommend that users sequence a part sample themselves before using it.


What does a sequence result of "Long Part" mean?

The Registry currently uses Sanger sequencing for quality control, and uses the VF2 and VR primer sites on pSB1C3, to sequence into the part. These reads are generally 600-1000bp long, and as such, we usually do not have full coverage for parts greater than 1600bp.

Please see Quality Control for more information.



Requesting Parts

iGEM HQ and the iGEM Registry no longer prepares and ships part and component requests to teams and labs.
Information related to part and component requests on the Registry and other iGEM pages is either deprecated or kept for archival purposes.

We encourage our iGEM teams to use our sponsor synthesis offers to synthesize the samples you need, or to find them through the iGEM distribution kits, if available.


How do I request a part?

You must be a member of a current iGEM Team or Lab to request parts.

Short answer: contact hq (at) igem . org with...

  • Subject: "Part Request: [Your Team/Lab's Name]."
  • Part Name (BBa...)
  • Plasmid Backbone (as documented on the Get This Part page)
  • Sample Location: source plate and well
  • Quality Control Results: sequence and gel results (if available)

Please see the Requesting Parts help page for more information


What are the costs associated with a part request?

As a registered iGEM team or lab, iGEM HQ covers the costs associated with material, labor, and shipping part requests.

However, iGEM does not cover any customs fees incurred when shipping to your country.

Please see the Requesting Parts help page for more information


How long will it take to get my request?

Once a request is made you should be contacted by iGEM HQ within two business days. Your request will then be entered into our request queue.

Shipping times will depend on location, but you will receive a confirmation email with a tracking number for your request.

Please see the Requesting Parts help page for more information. If you've submitted a request you can check on its progress in the request queue.


How are part requests sent?

We send out part requests as agar stabs (LB agar). The shelf life of these are short, so it is best to plate from the stab as soon as possible. Part requests are not sent on ice.

Unfortunately, at this time we cannot accommodate specific preparation for requests. This includes providing requests as miniprepped DNA, PCR product, etc.

Please see the Requesting Parts help page for more information


What E. coli strain will the part sample be in?

We store and ship our samples in NEB 10-beta cells.


Can I request a specific E. coli strain?

The Registry does not maintain any E. coli strains, aside from NEB 10b.


Can I choose the plasmid backbone for the part I'm requesting? I want BBa______ in pSB______.

You may find a part that has multiple samples in different plasmid backbones. If so, feel free to request a specific sample (be sure to pick the sample with the best quality control!).

However, if a part sample does not yet exist in the backbone of your choice, we are currently unable to transfer it to your preferred backbone.


Can I request primers for sequencing or PCR?

The Registry does not make or send primers by request.


Is there a limit to how many parts I can request?

Currently, there are no limits on how many parts can be requested, and how many separate requests can be made.

However, before making a request, please consider all of the parts that your group needs. We prefer bundling part requests together rather than receiving several small requests, as this cuts down shipping costs and improves efficiency.

Please see the Requesting Parts help page for more information



Adding Parts

What's the difference between a basic and composite part?

  • Basic Parts are discrete functional units of DNA. They cannot be subdivided into smaller component parts.
  • Composite Parts are functional units made from an ordered series of basic parts or other composite parts.

In order to create a composite part, each basic part that composes it must already be added and documented to the Registry.


Can I add RNA parts or Proteins (AA)?

No the Registry only accepts DNA. For RNA, you would use the DNA sequence that transcribes your RNA sequence, and give it a part type of RNA.


Tip: Avoid special characters when adding a part

Special characters like ' / - _ in the short description may cause issues with generating the part pages.


How do I delete a part?

You can delete a part by going to a part's "Information" page and setting the DNA status to "deleted".


I synthesized my entire device. Can I add it as a basic part and give it the correct part type?

No, this should be added as a composite part. You should make sure that the basic parts that compose these parts are on the Registry (already exist or you'll be adding them as new basic parts if necessary). You can can go to part tools > edit sequence and features and generate your composite part without BioBrick scars (Blunt Assembly). You can create a small basic part(s) with a part type of "Scar," and enter those in between the basic parts that constitute your composite part.


I want to add a part but do not know the sequence

All users should know their part's sequence before working with it. However, you can still add and document your part and add/edit the sequence later by going to part tools >> edit sequence and features.


How do I document an improvement on an existing part on the Registry?

There are many different ways to improve an existing part, from adding measurement data to codon-optimization. Please see our help page on contributions. Note that the following page is on how to document different types of contributions or improvements. Make sure to read through the medal criteria for a given iGEM year to understand what the judges are looking for.


How do I see if my part is compatible?

The Sequence & Features box will show you assembly compatibility.

The Assembly Compatibility checks that a part will meet the requirements for the Registry's supported assembly standards. It will show if there are any illegal restriction sites for a part. The above image shows a basic part the is compatible with RFC 10 and 1000, amongst others.


Note: All parts submitted to the Registry for competition evaluation (medal criteria, awards) must be BioBrick (RFC[10] compatible or Type IIS RFC[1000], unless an exemption has been given.

See the competition delivearbles page for part requirements


We have a part that we'd like to add, but it is not BioBrick RFC10 compatible or iGEM Type IIS compatible

Yes, please add and document it on the Registry. But make sure to see the parts deliverables page for competition requirements.


Should I include the BioBrick prefix and suffix or iGEM Type IIS prefix and suffix in my part's sequence?

No, your part's sequence should not include the prefix and suffix. While your parts should be assembly compatible, the prefix and suffix are an element of the plasmid backbone, not the part.


How do I upload images to part pages

Use uploads.igem.org to access your upload space. You can then use html tags in the wiki code:

< html ><img src = "url goes here">< /html > (removing the spaces in the html tags)


I have made a part, but cannot edit a wiki page

Make sure to follow the login instructions here, as you need to login to igem.org, and then into the part wiki.



Part Pages

What does twin mean on the Part Status Box?

Two or more parts are twins if they have the same sequence. The Registry is phasing out twins. If you're adding a new part, it should not be a twin of an existing part.

If you believe you have an exception, please contac us.


What does "released" mean on the Part Status Box?

The release system is currently only in use by iGEM HQ, so don't worry about it now! The Registry is introducing the concept of "Releasing a Part." This means that the author of the part says it is ready and important; its documentation and measurement are complete.


On a part's Sequence and Features box, what does the "View Plasmid" LabGenius-View Plasmid.png button do?

The plasmid viewer is a third party plugin, developed by LabGenius, for viewing parts in a circularized plasmid. It is for part and plasmid backbone visualization purposes. It is not indicative of sample (physical DNA) availability.



Part Contribution

Where should I document my contribution?

Your contribution should be documented on the existing part's main page (this is what all Registry users will see first!).

We are creating a minor change to the sequence of an existing part, should we add it as a new part?

Yes. If you are changing, adding, or removing a single base from an existing part, then you are creating a new part. You should add this to the Registry as a new part, and during documentation reference the original part, while also documenting your new part as a contribution on the original part page.

I've made a contribution, will this count as an improvement for the ____ medal/award criteria?

iGEM HQ & the Registry is independent of the competition judging process. All judging is left up to the judges, so we cannot say how a part or part contribution will be considered. Please note that any advice iGEM HQ gives on parts or part contributions, does not ensure fulfillment of medal/awards criteria, nor will it guarantee a medal/award.

We don't know if our work with an existing part counts as a contribution

If your contribution does not fall under the types mentioned, send us an email! We will give you as much insight as we can, but be aware that a final determination will only be made by the judges at the Jamboree.

I've made a contribution, but cannot upload the ____ file type to the Registry?

Send us an email! We'd be happy to answer your question.


Part Submission

Requirements

Sample submission of parts is no longer a requirement for the iGEM competition. Also, iGEM HQ can no longer accept shipment of samples. Please do not ship any samples to our offices. Information in regards to shipping of samples to iGEM HQ has been kept solely for archival and consistency purposes.

Parts must still be documented on the Registry and follow the guidelines/requirements of the iGEM competition.

What are the requirements for submitting a part sample to the Registry?

The requirements for submission...

Please see the Registry's submission requirements page for more information.

Why do parts sent to the Registry need to be BioBrick RFC10 or Type IIS compatible

iGEM and the Registry are built on standard parts which is vital to making biology easier (and more predictable) to engineer, for high school teams & university teams to research labs. It is also why iGEM has made BioBrick RFC10 and iGEM Type IIS compatibility a requirement; the parts that we receive from teams and labs can be used and assembled by everyone easily and reliably, without the need to substantially alter, experiment, or research alternate methods.


Does the Registry allow other Assembly Standards for parts?

For iGEM teams, only BioBrick RFC10 and iGEM Type IIS compatible parts will fulfill medal requirements and be eligible for awards.

However, you can add parts that aren't compatible with those two standards to the Registry. The Registry supports multiple assembly standards and is also open to integrating new ones. You can easily see what Registry supported assembly standards your part is compatible with, by taking a look at the Sequence & Features box.


My part is not BioBrick compatible

Before working with your part in the lab (characterizing/measuring), make sure it is BioBrick compatible. If not...

  • Synthesize your part to remove any illegal restriction sites, through synonymous substitutions (silent mutations).
  • Use site-specific mutagenesis to remove any illegal restriction sites, through synonymous substitutions (silent mutations).

Currently, the Registry only accepts parts samples that are BioBrick compatible. If you have questions about this requirement, please don't hesitate to contact iGEM HQ (hq (at) igem . org)! Contact us early and we may be able to address your concerns.


Why do my parts need to be submitted in pSB1C3

Having a shipping standard backbone lets the Registry receive and handle all parts in the same way: using the same growth conditions and quality control measures. With over 1000 new parts submitted each year, this improves our ability to handle, maintain, and test new parts. When anyone uses the part, they'll know exactly what to expect. They can easily unpackage it from the shipping plasmid backbone, and transfer it into a different backbone for a specific use.

Shipping in pSB1C3 ensures...

  • Your part sample will be flanked by the BioBrick prefix and suffix on the backbone
  • users can assemble these parts with 3A Assembly to build new devices and projects
  • The Registry can test and maintain all parts in the same way (sequence all parts using VF2 and VR primer sites).
  • pSB1C3 is a high-copy plasmid, which improves miniprep yields for parts
  • part samples can be easily moved from one plasmid backbone to another (for shipping, measurement, operation etc.)


My part cannot be submitted in pSB1C3 because of ______

First, contact iGEM HQ (hq (at) igem . org)! Contact us early and we may be able to address your concerns.

There may be a reason why a part sample cannot be submitted in pSB1C3. For example...

  • The part contains chloramphenicol resistance. Contact iGEM HQ first. You must use pSB1K3 instead.
  • The part is toxic to cells in a high copy plasmid backbone. Contact iGEM HQ first. You must use pSB3C5 instead.


My part is not meant to be used/operated in pSB1C3, can I use ______ instead

Unfortunately, no. Please remember, that the shipping standard backbone lets the Registry receive and handle all parts in the same way. In turn, when these samples are distributed to users, they'll know exactly what to expect. They can easily unpackage it from the shipping plasmid backbone, and transfer it into a different backbone for a specific use.


We've created a new plasmid backbone. How can we submit it to the Registry?

While the Registry does not specialize in plasmids, you can send your plasmid backbone with BBa_J04450, the Registry's default insert. Your plasmid backbone must be able to replicate in E. coli.

Please contact the Registry prior to plasmid backbone submission.

If you are an iGEM team planning on nominating a plasmid backbone for medals/awards, please be aware that the judging form system is looking specifically for parts.


Can we send part samples after the deadline?

There is no longer a shipping deadline for part samples for the 2019 Competition.

If you're an iGEM Lab, you can send part samples at anytime.


Formats

How do I prepare my submission for the Registry?

The Registry accepts part samples as dried down plasmid DNA in 96 well format. We provide a submission kit to all iGEM teams with the necessary material to ship their part samples to us.

Please see our submission kit page for more information.


Can I prepare my submission on filter paper?

The Registry no longer accepts filter paper submissions.

Please see our submission kit page for more information.


Other

I would like to send a part sample, but it requires an MTA

Please read the terms of your MTA, as this can vary case by case. While you can still add and document your part on the Registry, iGEM does not abide by any MTA, so we cannot accept part samples that require one.

I would like to send a part sample for a part that is patented

The Registry is open source, we do not take a position on IP on our parts. We don't publish any data on the state of patents and we make no claims about being able to use DNA from the Registry in commercial applications.


Software

I'm interested in creating software that interfaces with the Registry

We are currently evaluating the resources that we will open up to the community. In the meantime, please see our Registry API page.


I've created a software tool for the Registry

That's great! Please contact hq (at) igem . org, and tell us about it. We will see how we can incorporate the tool into the Registry, if possible.