Team:METU Turkey Software/test

Team

METU Turkey Software is an interdisciplinary team of 8 students and 3 advisors from various backgrounds such as Molecular Biology, Bioinformatics, Computer Engineering and Computer Education and Instructional Technology. We have put our knowledge and experience in our fields together to bring a much needed solution to a daily problem in field of synthetic biology for iGEM 2010

Motivation

Since 2008, we have been participating in iGEM as METU ( Middle East Technical University) wet-lab team, and each year we have noticed the increasing number of teams participating, along with an increase in biobricks entries at partregistry.org. While having more choices of biobricks to choose from is incredible, searching for and choosing the appropriate parts is becoming a challenge. This year during the construction process of iGEM biobrick parts for our new project, we felt the need for an application to find interacting parts based on an input/output model to design the genetic constructs. Using a specialized software for searching the parts registry to find possible biobricks to include into our construct would be much easy, fast and accurate than manual. We have shared our need with a group of friends who are software engineers, and initiated the METU_Turkey_SOFTWARE team where we worked together over this summer to build the BIO-Guide software.

Scope and Future Aspects

The partregistry.org is a continuously growing collection of standard genetic parts that can be mixed and matched to build synthetic biology devices and systems. The Registry is based on the principle of "get some, give some". Registry users benefit from using the parts and information available in the Registry for designing their own genetically engineered biological systems. In exchange, the expectation is that Registry users will contribute back to the information and the data on existing parts and will submit new parts they have designed in order to improve this community resource.

As an expanding database partregistry.org needs to be more organized and the standardization template needs to be improved. Additionally, the potential of multiple ways of using each part in different construct combination brings out the necessity for an application to search through the database. BioGuide is the first designed software that organizes over 1000 parts in partregistry.org as possible atomics parts to build new biological device and systems for specific input and outputs based on graph theory. The requirement of similar applications and software tools are now inevitable in the emerging field of synthetic biology. The innovative approach that makes the partregistry.org easy to use for synthetic biology applications is the collection of standardized parts that can be used in any combination with minimal effort under one database. But while working on our algorithm to search for possible combinations of parts depending on the given input and output, we have realized that present standards are inadequate and parts registry form must be improved.

In very near future a new format for parts registry form is needed and few additional features should be implemented to have more control on the database. We are planning to suggest a new format and features for the parts registry based on the survey results we have received. And planning to build the next version of Bioguide based on the revised parts registry form. Along with using new parts registry standards we will be improving the algorithm, so that the software can search through more complex relations and returns all possible functional constructs.

Project Introduction

As the field of Synthetic Biology is on the rise, iGEM is growing up very fast and the number of parts in the parts registry is increasing with the addition of more complex parts each day. After facing some difficulty while running our algorithms on the parts registry, the need for more effective standardization of parts entry was apparent. We have investigated the information on parts in iGEM’s 2010 distribution and reorganized the information on the parts registry forms according to the needs of our algorithm. Then we have used graph theoretic modeling to visualize the relations between iGEM Parts and to standardize the representation of the parts as much as possible by graph theoretical methods. This helped us to find input output relations between the parts. Furthermore, our program BioGuide is now able to provide alternative pathways to construct the most reliable and functional Biobrick devices with respect to given inputs and expected outputs as a guide to Biobricks parts registry.

Notebook

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Collaboration

Part Registry Survey

Click here to go to survey page..

Results

(including responses between 10th -22nd of Oct 2010)

General Profile of Participants

• The following teams are dedicated as collaborators with more than 60% team participation are
• INSA-Lyon
• Lethbridge
• WashU
• Out of 244 participants between 10 to 22.10.2010, 57% of the participant had scientific degrees from B.Sc to Professor and 18% had graduate degrees. 18% of participants are enrolled in their teams as either Instructors or Advisors.
• 95 teams have responded to the survey while we are still waiting to hear from 33 teams. 74% teams participated with one or more members to the survey.
• 75% of participants were interested with synthetic biology field for academic purposes.

Browsing the Registry of Standard Parts

• 56% of participants think that it is not easy to search for the parts in Registry of Standard Parts. Many comments indicate a need for a better search engine and more flexible keyword search options, especially excepting aliases. Also many are longing for recognizable parts names, which will ease searching with keyword.

Partnership with Google and enforcing standardized parts names are suggested

As a global organization iGEM can offer the Parts Registry in different languages and more illustrations describing how the system works.

Content of Registry of Standard Parts

• 57% of participants agree that the number of parts registered in the Registry of Standard Parts is not enough for their projects.
• 55% of participants think that there are enough and useful parts distributed in iGEM Plates that we can use in our projects.

Even though most agree the number of parts in the registry is impressive, still they find it limited when it comes to design different devices for diverse applications especially in different species other than E. Coli. Participants believe that if there are more functional standardized parts, especially protein coding sequences and promoter-RBS , they can design devices according to the needs of the community instead of designing what can simply be assembled into a device.

Encouraging development of vectors and standards for new species and new standardized parts in different research areas is suggested.

Enforcing submission of right DNA sequences and working conditions for each part is suggested.

Few recommend expanding iGEM into a collaborative effort rather than an undergraduate tournament, which will increase the number and the diversity of the parts designed and submitted all throughout the year.

Submission to the Parts Registry

• 52% of participants said that they have not encountered difficulties during submitting parts. Even though participants are satisfied with the web interface of the registry, most complains about the pSB1C3 as the new standard plasmid to submit DNA.
• 71% of participants are like minded with our team's opinion, which is that The nomenclature of part IDs such as construct, device, composite parts, protein generator, is confusing as there is no consensus on how to use them correctly.

Terminology and categorization used on iGEM’s Parts Registry should be re-described and correct use of terminology should be enforced during the submission process.

• 75% of participants agree that different, specified submission interfaces should be designed for contructs, promoter, RBS, CDS and terminals is needed during Registry of Standard Parts. But, there are very strong and valid arguments against it such as, losing the flexibility of the registry will not allow future submission of unclassified parts.

We suggest keeping the parts submission interface as is, until these concerns are addressed.

• 75% of participants agree that Out-dated, un-available and not-characterized parts in the Registry of Standard Parts should be removed to an archive after the consent of the designer.

“It would be great to see some sort of organization like this! I agree that unavailable parts should be followed up on and removed if necessary. I also think that parts which are not sufficiently documented should be highlighted in some way. Once these parts are identified, teams can actively characterize them as part of their projects or as side projects.”

“Think about these things: (i) who decides when a part is out-dated, and how can that person know that an old part cannot have a novel use in the future? (ii) likewise, an uncharacterized part may be both characterized and used in the future”

We suggest building a backup system, such as an archive, to sort out the rarely used, un-available and un-categorized parts until they are in line with the enforced standards.

• 91% of participants have same opinion with us, which is that standardization of the nomenclatures used for each different composition of parts is necessary.

Standards that should be enforced and Additional New Standards

According to our survey, from high rated to low, these standards have been rated which has been used while assigning a name to parts

• 33% Type of part
• 17% Input
• 17% Output
• 14% Version
• 10% Year
• 9% Group

Along with above, having short recognizable part names along with function and performance , Genbank/EMBL link and organism information is important.

• 93% of participants have said that for the parts that are marked as “WORKS” distinguishing the parts with quantitative experimental validation vs parts without this information is important. Most participants have encountered with similar problems about parts that don’t work under their lab conditions or works but not they were claimed for.
• 89% of participants have same opinion with us, which is that iGEM should sub-categorize the “WORKS” comment into 1) “Quantitative” for parts which are characterized with experiments and 2) “Qualitative” for parts which are not characterized will be an appropriate measure for standardization of Biobrick database.

In order to overcome these problems we suggest enforcing the working conditions title for the registry entrance, in order to collect quantitative experimental details on submitted parts, which might slow down the registration process but will definitely increase the quality of the database.

• 61% of participants agree that POPS (Polymerase Per Second) should be assigned to every part or biobricks with a promoter, where appropriate. - 57% of participants have been agree that RIPS (Ribosome per Second) should be assigned to every part or biobricks with a RBS brick.

Though most participants agree the need for POPS and RBS information , they are concerned about the workload it would bring to individual labs.

“To do this, the Registry need to define a reliable and easy method of determining the PoPS for teams to use. However, I would say that there are better systems for quantifying promoter output than PoPS, and they should be used instead, if possible”.

• 67% of participants have thought that entering POPS information should not be mandatory while submitting new parts. Similarly, 65% of participants disagree that entering RIBS information should be mandatory while submitting new parts

Even though the researchers feeling the need for this information they are shying away from requesting it as a mandatory title for parts registry as it would be difficult for underfunded and inexperienced groups to perform these measurements.

We strongly suggest starting a forum on how to quantify the performance of promoters and genes to bring an easy to measure standard for the efficiency of the parts. Additionally iGEM should the responsibility and provide the measurements for the each promoter and gene included in the distributions. The second choice would be even better in terms of standardization as all the measurement will be performed by one center under similar conditions and with experienced researchers, which will allow user to compare and contrast the efficiencies of the parts more accurately.

• 82% of participants have thought that information on working conditions of the parts should be mandatory while submitting new parts. Most find submiting the detailed experimental information and working conditions is crucial and even easier than submitting measurements of POPS or RBS.

Definitions you would like to see at the Registry of Standard Parts

• Transcriptional efficiency 13%
• Protein lifetime 10%
• Ribosome binding efficiency 10%
• mRNA lifetime 9%
• Translation initiation and efficiency 9%
• Protein concentration 9%
• Cooperative effects with other molecules 9%
• Protein-DNA binding rates and efficiencies 8%
• RNA polymerase affects 8%
• System copy count 8%
• Protein multimerization 6%

Additional titles includes: Catalytic rates and affinities for substrates, leakiness of promoter in lack of stimulus, POPS at various inducer/repressor concentrations.

Efficiency of the Database Entries

• 86% of participants would like to see a ranking/rating system for the parts by the other iGEM users which will be one indication of if a part is working and how well in different laboratories. Few had concerns about how well the rating system will work for rarely used parts while the widely used parts would even more popular due the the rating system. Still many believes this would be one futher towards a peer-reviewed quality control system for the parts.
• 61% of participants agreed that parts should be updated regularly by the designers, where most agreed at least when there is new information on the parts. It has also been suggested to give permission to all the users of that part for updating information.
• 73% of participants have been agree with us that excluding the low ranking parts or the parts with negative feedback from the future plates will increase efficiency of the system. The major concern about excluding any part is losing the variety of parts in the database. Few recommends excluding only the parts that are not working.

“Efficiency shouldn't be top priority in a database. First and foremost, data is the top priority. Excluding those parts would make the system more efficient”

“Some parts may be rare or new and have low efficiency, but can be very important! Getting rid of them would eliminate any chance of improvement to these parts, which not only a qualifier for an iGEM gold medal, but also one of the focuses of biobricks.”

We suggest excluding the parts not-working, low rated or with negative feedbacks from the annual distribution plates but still archive them and make their data available through the parts registry. So the while the individuals labs are receiving plates with higher rated, fully working parts for their projects, anyone who wants to work on a more exotic part can search through the achieves and re-vitalize the parts stored there. The challenge of re-vitalization of parts can be encouraged as an collaborative effort.

New Options for the Parts Registry Database

• 96% of participants are like minded with us that it will be useful to have a link out to the gene/protein information of the parts and - %97 of participants have been agree that they would like to know if a part is also involved in known biological pathways.

For receiving pathway information more participants have voted for NCBI Cog (59%) than KEGG pathways (38%) when the responses for both has been distributed among the choices according to response rates. Adding the blast option to the parts registry has also been suggested to locate parts of interest. We are sure all of us would like to see gene-protein and pathway information if these information was integrated into the database and offered automatically for each entry in the database.

We are planning to provide this information about the parts to all parts registry users as a build-in option in the next version of BioGuide in iGEM 2011.

New Parts Registry Form Suggested for The New Standards

Description

Warning Boxes:

• If Out-dated, un-available and not-characterized parts exist in the Registry of Standard Parts, bring to an archive after the consent of the designer. Divide archive into three title: Out-dated, un-available and not-characterized parts
• Besides shown as “works”, in the works box there should be explanation whether the part is characterized or non-characterized.
• Parts should be updated regularly by the designers
• Excluding the low ranking parts or the parts with negative feedback from the future plates

Characterization Boxes:

• transcriptional efficiency
• mRNA lifetime
• ribosome binding efficiency
• translation initiation and efficiency
• protein lifetime
• protein concentration
• protein multimerization
• protein-DNA binding rates and efficiencies
• cooperative effects with other molecules
• RNA polymerase effects
• system copy count

Desription

Search box

• with click options
• options: searched parts are:
  • Available
  • Length OK
  • Building
  • Planning
  • Missing
  • Unavailable

according to the clicks of above options, search is modified

Description

Assume on the part image;

• part DNA sequence is not confirmed, then tag with "non-confirmed DNA sequence"
• non-characterized parts in the Parts Registry are not characterized further, then it will be tagged as "deprecated"

also:

• comment box stated that any team can make comment about experiences with the part is opened
• boxes which had been not filled with the data are highlighted;
  • transcriptional efficiency
  • mRNA lifetime
  • ribosome binding efficiency
  • translation initiation and efficiency
  • protein lifetime
  • protein concentration
  • protein multimerization
  • protein-DNA binding rates and efficiencies
  • cooperative effects with other molecules
  • RNA polymerase effects
  • system copy count
• if the part is not characterized but "works" then a "Qualitative part" tag is added
• besides "works", "Characterized" or "non-characterized" box is added
• ranking/rating stars for the parts voted by the other iGEM users which indicate how well the parts perform in different laboratories is added. For example 4.5 star voted by 27 teams (number of stars and number of votes)