Team:HFUT-China/Proof
Feedback
To prove the utility of our software, we released the 2.0 version of BioDesigner Coral and invited several wet teams to use it. We want to inspect whether it can solve problems under real-life condition, as well as collect synthetic biology researchers’ opinions on computer-based literature analysis. Wet teams are asked to fill in a questionnaire about BioDesigner Coral： see^_^ Here are the results:
Remarks & Suggestions:
Haoran Ding from TJU: Overall the software is excellent. We tried to use this software to build a part we use this year and search for some genes we often use. I search for PET degradation, which is our topic this year, and I really get the relative part. I guess it is the first software focusing on the searching of iGEM part. I think what they need to do next is enlarge the database, update the new parts this year and further improve the accuracy of recommendation.
Yisi Wang from OUC-China: I like the concise user-interface of the software, because I can easily understand the relationship between parts and parts information. Most of the standard parts are stored in the database. For the next version of the software, I think they can try to allow users to upload their own parts to the database, so there will be more non-standard parts. Besides, I think it is a good idea to collect some experimental data about some parts for more optimal protocol.
Yu Zhu from XMU-China: The design page leaves a deep impression on me. But I think it would be more user-friendly there is a return button on this page, so users can go back to the last operation. Personally, I think the gene relationship map is not beautiful enough. Can you change the color of lines between genes from black to others?
Kaiyue Ma from USTC: Generally the operator interface is concise. I have not tried to test the function of other database, and I think that of BioDesigner Coral is OK. But I think the user interaction can be refined in many ways, for example, after registration, the web page should automatically turn to the log in page.
Fankang Meng from NKU: I am interested in Gene Relationship network. However, the names of genes on this map can be put at more reasonable positions, so the network will be more beautiful. To further improve the software, I think they can refer to software in Wikipedia, which has similar functions. And the database of Gene Relationship should be expanded.
recall (also known as sensitivity) is the fraction of relevant instances that are retrieved.
For example for text search on a set of documents recall is the number of correct results divided by the number of results that should have been returned In binary classification, recall is called sensitivity. So it can be looked at as the probability that a relevant document is retrieved by the query. It is trivial to achieve recall of 100% by returning all documents in response to any query. Therefore, recall alone is not enough but one needs to measure the number of non-relevant documents also, for example by computing the precision. we trained a markov model to recommand DNA ceil on our platform and these recall rate values show the sensitivity of the markov model when it return different length of the DNA chain.
