"

From 2011.igem.org

The aim of this project is to provide a software tool for wet-lab biologists to facilitate the process of choosing the appropriate parts to use in their experiments in minimum amount of time and effort. It is always challenging for wet-lab biologists to pick the right parts to make a working device that satisfies their demand, for solving this issue, our team decided to prepare a software that enables wet-lab biologists to easily pass their desired input and output to this software and observing the predicted pathways which are activated by the input and produce the requested output. Our software can also rank the DNA constructs based on the popularity of biobricks and the frequency of their usage. By this way, our software proposes a method which can be utilized in pre-experimental step as a supporter DNA design tool.

Safety is always a concern in synthetic biology, computer applications and virtualizing techniques tries to reduce the threat of non-predictable events. We can safely say that "we are as safe as the Parts Registry database." We do not use any information or part that is not already available in the parts registry database. Whatever new "constructs/devices" Mining for BioBricks (M4B) software generates can also be generated manually by browsing the parts registry. We do not build or test these devices and provide purely "information" to biologists. The Mining for BioBricks (M4B) software we are developing is only intended to use for research purposes and no clinical or military application is supported by METU-BIN Team.

• 1- As a pure software team we are, our materials used for project or final products are not in any biohazard classification. Middle East Technical University complies with all regulations about office health and safety as required by Turkish Office of Safety and Health at Work (OSHA). Safety and health issues that might be a concern for METU-BIN Team members can be addressed with general precautions for office workers, such as not working long hours in front of the computer screen, taking frequent, short breaks, using ergonomic equipment, changing position and posture to ease the pressure on certain joints and adding an exercise routine into their breaks to strengthen their posture.
• 2- The standard questions in the questionnaire about safety are not applicable to "software" projects as our project doesn’t require any biological laboratory work and we won’t be submitting any parts to the Registry.
• 3- METU-BIN Team is supported by the Bioinformatics Program at METU Informatics Institute. Even though we are not a biological or natural sciences department we are doing our best to act within the national biosafety regulations our university has to comply with, which can be found under
  
  http://www.ttb.org.tr/mevzuat/index.php?option=com_content&view=article&id=753:bogenl-kanunu&catid=1:yasa&Itemid=28
• 4- Our software tool, Mining for BioBricks (M4B), will be providing in-silico blueprints for new devices that can be built by using DNA constructs in iGEM’s 2011 plate distributions. Even though we won’t be physically providing the constructs to researchers, we have been brainstorming on how to make Parts Registry safer and secure, which in return can minimize the unintended use of the software we have been developing for efficient use of the parts database. Classification of biobricks in the Parts Registry with gene products that are pathogenic, infective or toxic with potential threats to researchers, public health and environment are some of our main suggestions. When this information is available it can be integrated into the database search tools and users of the Parts Registry will be aware of the potential dangers of any biobrick they are planning to use in their devices. Some might argue that this classification might point to the candidate biobricks for misuse, but as METU-BIN Team we support that the researchers should be informed about the potential threats of the parts and this information should be easy to access so that they can take precautions for their designs.

Any information needs to turn into action to become an actual threat as in garage bioterrorism. But one would need to physically access to the biobricks distributed through iGEM’s Parts Registry, so increased security measures to control, screen and follow the laboratories, which requests biobricks and registering users, is a natural start point for a more safer Parts Registry. As an initial precaution to make our software, M4B, safer we will be following the users of our software by their IPs and if needed we can restrict access to our software website to academic users or to only iGEM registered laboratories. If a list of high risk IPs is provided to us by iGEM we can cross-check our users in real time and inform iGEM about these suspicious activities. In addition, if the biobricks in the registry are classified by iGEM, we can keep the list of users whose search involves high risk biobricks or the search results with devices which includes potentially hazardous subparts and track the access of these users to our server site to inform iGEM.

At the same time, we are aware of the fact that iGEM’s biobrick distributions are not the only source of devices that are built with synthetic biology techniques. Most molecular biology laboratories would have the capability of building biobricks and devices as in the Parts Registry. So, any new security measure on access to the Parts Registry and to our server site to use M4B should not be a restrain on researchers, should support the creative side of the synthetic biology, aiding to the new innovations in the field.