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Team:Wellesley HCI/Notebook/NicoleNotebook
From 2012.igem.org
Nicole's Notebook
May 29: (Day 1) First day of the summer session!
Research started today, so a majority of the day was dedicated to administrative details about the program. Otherwise, Veronica and I were assigned to research more about semantic search--what it was, its benefits, and whether or not it would be worthwhile to pursue this field in the context of synthetic biology. We will be presenting our findings near the beginning of June.
May 30: (Day 2)
For the majority of the day, I was learning how to code with C# on a Windows 8 Surface. It was easy to get lost on the more technical side and details of the coding, especially because the instructions seemed to assume you knew about the basic commands in C#. Other than that, it was easier to delve into the code without blindly copying down if it had been my first time. There were a couple of times where getting stuck and being unable to figure out the problem because of my lack of knowledge got frustrating, but because it was my first experience creating code to manipulate objects on a touch screen, I found the learning experience to be pretty amazing overall. Otherwise, I’ve been doing more reading on synthetic biology. It took me a while to read them since I hadn’t taken up Biology since the ninth grade, but I found the idea of engineering a new biological function interesting so I managed to complete most of the reading.
May 31: (Day 3)
I continued reading more about Semantic Search and its advantages compared to other types of searches as well as its disadvantages along with exploring different semantic search engines that are already available on the web, specifically for bioinformatic research (e.g. [http://bio2rdf.org], [http://distilbio.com], and [http://nlmplus.com]). A couple of papers also introduced me to the idea of incorporating other types of searches in Semantic Search. I learned a bit more about text mining, natural language processing (NLP), and ontology.
June 4: (Day 5)
Veronica and I continued reasearching on Semantic Search for the morning. The lab then headed over to Microsoft NERD for the second half of the day where we learned about their new beta project, a tablet with Microsoft 8. The interface is definitely engaging, what with their idea of using tiles and semantic zooming. I also like how transparent they’re trying to be with people who are trying to create applications for their story. Their idea of using a picture the owner can choose on their own as part of the password was really cool! I also like how they found a way to accommodate different finger sizes by enabling users to rescale the keyboard. All the different gestures to fully use the tablet however are not intuitive and takes some getting used to. It seemed much easier when Edwin was just demonstrating the product for us than when I actually tested out the tablet myself. Although, it is great how applications can now be made using HTML5 and JavaScript. I'm definitely going to start learning how to code in these languages before the summer is out.
June 5: (Day 6) A day in the wet lab
The lab met up in MIT and we spent the entire day learning more about synthetic biology. Professor Natalie Kuldell gave us a lecture in the morning and had us running experiments that afternoon to try applying what we've learned and get us exposed to the lab environment (which was particularly helpful for those of us who hadn't done Biology since 9th grade). Natalie was able to make the lecture engaging when talking about the basics of synthetic biology and its similarities with other engineering practices. Once she got more technical however it was more difficult for me to follow. As for the lab, first of all, I've definitely gained a newfound respect for people majoring in the biological sciences. Lab can be very tiring--and we were only in there for two hours when labs in Wellesley College courses usually take 4+ hours!
It was difficult to remember reasons behind you're doing the protocols you're doing especially if, like me, one is a beginner in the subject who's more immediately concerned with what the lab procedures mean by using a certain instrument or machine to complete a protocol. It was helpful that Natalie had led us into a discussions after the lab to reflect on what we just did and sort of touch upon the big picture, but I definitely felt like, by the end of the day, I learned more about lab processes rather than the material that motivated the experiments in the first place. Natalie highlighted how difficult it is to look for information when the researcher does not know what to look for--something that hopefully we'll be able to facilitate using the applications we'll be developing for iGEM and semantic search.
June 6 - 8: (Days 7 - 9) Preparing for Presentations
Veronica, Casey, and I discussed our individual findings from the research we had done until this point and decided what we'd be presenting -- the basics of semantic search, ways we can implement semantic search in surface applications, and challenges of implementing semantic search. We also tried finding an already made API we could customize because creating our own semantic search engine is definitely not a feasible job for a few people in one summer.
We spoke with Consuelo and Orit about our current material for our presentation this coming Monday and found that we needed to research more on the feasibility of implementing a customized semantic search engine using databases like PubMed, iGEM, and the Parts Registry. We then finalized our presentation.
On Friday, we were able to speak with Professor Eni Mustafaraj. She went over a brief explanation of semantic search and how it is implemented. She gave us suggestions on ways we could have our own customized semantic search engine. Initially, we had thought of using the commercially-made engines that enabled users to modify it based on the databases they want the engine to use. Eni warned us however that we should search for semantic search engines that had been written about in a research/academic paper, and instead pointed us towards an open source project called Apache Jena. What we would have to do is somehow convert what we want into RDF format and from there figure out how we could implement the engine using Jena.
June 11: (Day 10) Presentation Day!
Today, each group presented their findings on the topics we had been assigned at the beginning of summer research. Between each presentation, we shared ideas that popped into our heads and devoted around 10 minutes to brainstorm how each of what had been researched could be integrated into our iGEM submission.
I found the idea of the DiamondSpin (i.e. the Lazy Suzanne for platforms) really interesting. It has several functions but I found it to be most intuitive for the windows to shrink as they were dragged towards the center. Then, should a person at the other end of the Beast, for example, want to access it, they would just use the outer rim of the circle to rotate it such that the window’s orientation would be adjusted appropriately and it was closer to them. Then, they’d be able to drag it outside the circle and examine it. As for the idea of windows getting larger as they were dragged towards the center, while this may seem useful for presentations, considering that the circular form makes sense for a platform with people surrounding it like the Beast (change in orientations), then enlarging it in the middle to present it to people would keep it in one orientation. Consequently, the orientation may be readjusted enough times that it would become a distraction during the presentation.
After the presentations, we were split up into two different groups and each came up with five different big ideas for projects to pursue over the summer. I really liked the idea of having a graph, inspired by the idea of Semantic Search, that essentially tracked the person’s “trail of thought.” They begin with a main query that constitutes the middle bubble. Then, the succeeding nodes represent queries they made right after and/or related to the node it is attached to. If the person wanted to go back to change a query or start another trail, they’d be able to. There was also the idea of the personal lab helper (like the animated clip on Microsoft Word). The program would different between people by recognizing their irises or fingerprints to prevent confusion. The surface would be the lab table and through each protocol, if a certain tool was needed, the shape of the tool would appear on the surface and keep blinking until the person prepared the correct tool. A camera would be placed above the table and record while the researcher would be doing an experiment. There were also a lot of ideas for the eLab Notebook, like being able to zoom in to a protocol and annotate it but when you zoom out again, all that has changed is that the protocol is now either highlight or changed its color to red. The user would then know that they had annotations and there would be no clutter.
June 12: (Day 11) A day in the wet lab
The Wellesley Lab went over to Boston University. We were able to meet the two undergraduates who are part of the BU team. Traci presented more about Synthetic Biology and went into more details about parts names, what they did, and we learned more about what they are currently doing for the competition. Afterwards, three from the Wellesley team presented our research topics and the ideas that resulted from our brainstorming the day before. We then proceeded to brainstorm even more, gaining valuable insight from the BU team.
