User talk:Dondi
Hi Dr. Dionisio, I noticed that you minored in music! What is your favorite type of music and what instrument(s) do you play? Emmatyrnauer (talk) 20:41, 31 August 2017 (PDT)
The first question is hard to answer—I like all kinds of music! Classical, pop, rock, show tunes, electronic, jazz—at any given moment, I can be in the mood for any one of them. I guess I have a soft spot for early jazz and big band, because I like to dance to those. But really I have favorites across the board.
As for instruments, I mostly dabble, and can probably handle piano and guitar the most (no mastery, just some chords and rhythm).
Hello Dr. Dionisio, you mentioned how your loved for computers started with gaming. What was your favorite old-school video game? Zvanysse (talk) 00:37, 1 September 2017 (PDT)
How old school do you want to go? 😅 I’ve had a few phases even in old-school times, but most of the time I gravitated toward role-playing games; way way back I was captivated by Wizardry (Sir-Tech). A little later I moved to The Bard’s Tale then to the Baldurs Gate series. In between, I also took to the early real-time strategy games like Warcraft (the original series, not WoW) and StarCraft. First-person shooters didn’t hold my attention for very long, but I got deepest in with Bungie’s Marathon series.
Um, I better stop…
Hi Dr. Dioniso, I see you studied mainly computer science in college. Did you ever have an interest in biology before teaching this course? Mbalducc (talk) 14:28, 1 September 2017 (PDT)
I have always liked the sciences in general, but admittedly most of my exposure to biology has been due to my collaboration with Dr. Dahlquist. Before coming to LMU, I did some work in medical informatics at UCLA, so that was the closest prior background before bioinformatics.
Hey Dondi! What was the first computer language that you learned when you started studying computer science? Also what languages do you enjoy most, or find yourself using most, nowadays? Qlanners (talk) 11:25, 2 September 2017 (PDT)
My first programming language—as is the case for many in my age bracket—was BASIC. Yes that is an acronym! I learned this over summer in sixth grade, and one might say the rest is history. Something that appealed to me greatly about BASIC was that it was built in to most personal computers at the time; without needing to install anything new, you can type a BASIC command directly into the command line (which was the only interface available back then) and run some code right away.
The closest equivalent to that today is JavaScript, because it is present in every web browser today, and web browsers are pretty ubiquitous. You just need to press the correct key on the browser to get JavaScript to show up 🙂 But once you’re there, I get a lot of the same feeling that I used to get with BASIC.
Which I guess leads me to your second question—these days (not for the similarity to BASIC, but because it’s what web browsers run every day), JavaScript is perhaps my most frequently-used language. Python is a close second. Slightly further back is Java, which, despite the name, is actually quite different from JavaScript. Though not exactly the same kind of “language,” I also frequently write HTML, CSS, and SQL. For my upcoming sabbatical, I anticipate that I’ll get some good exposure to Swift. The learning never ends!
Hey Dondi! I wanted to ask you what your favorite part of computer science is. I noticed you started coding when you were in sixth grade. What appealed to you then and what still appeals to you now? Simonwro120 (talk) 16:49, 3 September 2017 (PDT)
I’ve always gravitated, and continue to gravitate, to anything in computer science that has a visual aspect. So for example it isn’t surprising that the courses I teach most often are Interaction Design and Computer Graphics. In that sense I haven’t really changed from early on, although I’ve certainly learned a lot more!
Hi Dondi! What is one thing you think every computer scientist should learn and/or know by the time they leave school to work out in the "real world"? Bhamilton18 (talk) 13:13, 4 September 2017 (PDT)
Arg, I’d love to say everything but I realize that’s kind of a non-answer. Let me answer in this way: there’s theory, and there’s practice. In the theory area, I think the one thing to take away is data structures and algorithms—what they are and how they are related. This underlies every other computer science endeavor.
However, you also talked about the real world, and because of that, I also can’t ignore practice. For that, I think a computer science graduate should definitely have a level of proficiency with just hands-on, head-down programming. People will not appreciate your theoretical knowledge unless you can put it to demonstrable use, and that is by writing code. It doesn’t matter what language (because that will change over time anyway)—just be proficient at something.
So I know you said one thing but in the end I couldn't really separate the two. Hope that’s OK.
Hello Dondi! I was wondering what is it like to work a for a technology company such as Friendbuy while working as a university professor. Is it difficult to manage several projects like that simultaneously? Johnllopez616 (talk) 16:02, 4 September 2017 (PDT)
There is some extra effort needed to keep both university and consulting concerns fulfilled, though when the semester is up and running, university matters get the clear priority and majority of the time. As such I sometimes fulfill less technical or time-consuming tasks as a consultant, such as conducting technical screening of candidates or discussing strategy with the company leadership. So overall it isn’t too onerous to juggle, and the net benefit, which is that I learn new things from both environments which I can then take to the other, really makes the overhead pay off. Much of how I structure course work is informed by the real-world industry practices that I encounter, and vice versa some of my research and academic knowledge helps me do a better job in industry plus assists in the professional development of junior developers on that end. So it’s a win-win situation overall.
Hi Dr. Dionisio! My question for you is what got you into teaching computer science? Did you always know you wanted to teach? Cwong34 (talk) 16:52, 4 September 2017 (PDT)
Teaching wasn't the first thing I had in mind when I got into computer science—I simply liked the subject matter, and happened to luck out that there was also high demand for it so parental units did not have any issues 😂—but as I spent more and more time in college, I started getting feedback that teaching may be a good fit for me. Conversely I also found that teaching-like activities—being a tutor, or TA, or lab assistant—generally appealed to me, so by the time I was out of grad school this was definitely in my radar. The final deciding factor was the opening of a position at LMU; when I heard about that, I saw that as an ideal way to finally take up teaching full-time.
Hello Dr. Dionisio, straying away from asking about computer science, what do you enjoy doing outside of LMU academics and video games? Though I've been here for three years, what would you suggest to someone who hasn't been to the LA area before? Aporras1 (talk) 18:03, 4 September 2017 (PDT)
I enjoy the usual banal delights 😈 —good food, drink, and company. I watch my share of mindless entertainment but probably not a lot compared to others. I enjoy big band and swing though that comes few and far between with my current schedule and obligations.
Segueing into your second question, I enjoy museums a lot; museums of all kinds. As such I would recommend LA’s broad selection of such places (no pun intended): LACMA, Natural History, the Page Museum, the two Getty’s, and most recently the Broad (explaining the potential but unintended pun). Further out there’s the Huntington, and though not strictly a museum, the Griffith Observatory has its share of worthy exhibits. So it might not be the most mainstream of LA things to do, but it’s what I enjoy.
Hey Dondi! Are you currently hooked on any video games? If so, where did you hear about it and what game is it? Ebachour (talk) 18:50, 4 September 2017 (PDT)
Haha it’s very dangerous for me to let myself get hooked on video games. I guess the most recent “hook” was actually a game that I had dropped for a while—Diablo III. I hadn’t touched it for years then heard that there was something special going on to commemorate its 20th (20th!) anniversary. So I had a bit of a homecoming to that for a time. But it’s been a few weeks since I’ve played it, or anything else; work just caught up with me.
On the newer end of the spectrum, I do have a stack of games that I’d like to eventually play, when I can manage to carve out the time. Injustice 2 and Tekken 7 are the recent ones; further back, I have yet to take on Arkham Knight and Skyrim. I was able to work my way through some of StarCraft 2 a few years ago but those expansion sets keep pushing me further behind. Probably a fairly pathetic list compared to folks who like to play and have the time for it!
Hi Dr. Dionisio, since you are a Batman fan, I was wondering wondering the following: are you primarily a fan of the the Batman comics or are you a fan of the movies too? If you are a movie fan, which film (or actor who portrays Batman) is your favorite? And who is your favorite Batman villain? Kwrigh35 (talk) 20:28, 4 September 2017 (PDT)
Yikes, another thing I can blab on about…my Batman trajectory is probably very similar to folks in my age bracket: my earliest exposure to Batman was the TV series starring Adam West (I did not realize until adulthood that the show was actually a comedy), then the various Superfriends cartoons of the late 1970s. High school/college was when I got into the comic book renditions; I still distinctly remember buying my copy of The Dark Knight Returns from Fox Hills Mall way back in its pre-pre-pre-Westfield renovation incarnation. By the time the Michael Keaton/Tim Burton films came out, followed by the Bruce Timm animated series in the early 1990s, I was already steeped in the mythology and watching those truly felt like watching the comic books and graphic novels come to life.
I have what is probably a very typical favorite—Christian Bale’s version, particularly in the second film, The Dark Knight. But I wish he had Kevin Conroy’s voice from the animated series. And I will have to admit, minus the massive firepower display, Ben Affleck’s hand-to-hand fight scenes are probably the closest to what I used to imagine a fight with Batman would look like.
Favorite Batman villain…agh that is hard. Catwoman is the first that comes to mind because she has some real complexity; she isn’t a flat-out villain. The animated series actually came up with a very compelling one, the Phantasm (see Mask of the Phantasm). But overall the rogues’ gallery is quite rich and at any given moment, any of them could also be a favorite.
Hi Dondi, How did you feel about the way lego batman was portrayed in the Lego Movie from a couple of years ago? Was his character too whimsical when compared to the "edgy" nature of batman as portrayed in the comics and movies? (also, slight note, but in your user profile you include a mailto link which is inconsistent from the rest of the wiki) Cazinge (talk) 22:55, 4 September 2017 (PDT)
I thought the Lego Batman portrayal was a fine satirical take on the character—he had some nice funny bits and the exaggerations were pretty on-point. Since my Batman exposure goes all the way back to the Adam West stuff, I’m pretty OK with these varying takes—kind of inevitable given the character’s pop culture exposure. I’m not one to cry outrage for that kind of thing 🙂
In terms of your note, did you mean how the email address is not modified or spelled out? I sort of just went with that because as it is, my email address is already on other public websites so there wasn’t much to protect there from scrapers. Or was there something else about it that’s off?
Hello Dondi! Is it okay if I call you Dr. Dondi? It keeps coming to mind when I think of your name, it's okay if not. What is your proudest moment in regards to computer science? It can be a recent accomplishment or idea, or something you'll never forget! Thanks, Hhinsch (talk) 23:39, 4 September 2017 (PDT)
“Dr. Dondi” is certainly OK, and you wouldn’t be the only one 😀 I spent a good chunk of my life working to get that title, so I definitely don’t mind hearing it, heh.
I think I’ll split my answer into two different kinds of “proudest moments.” On an intellectual/academic level, I think I’m proudest of getting published in one of computer science’s most prominent journals, ACM Computing Surveys. Not the catchiest name, but it is one of the oldest and widely read computer science publications out there. I co-wrote an article on virtual world applications and we submitted it to that journal solely as a moonshot, and to our ecstatic surprise it was accepted for publication. So I’m proud to have had my name appear at least once on that publication.
On a different level, I’m also proud of any time that software I write gets used in the real world. It won’t be anything like an Angry Birds or Candy Crush, but I’m happy just knowing that there is code out there, whether an open source project done for research or academics or portions of commercial code due to my consulting work, that is running and doing work for other people.
Hi Dr. Dionisio! Did your decide to work at LMU because of your undergraduate experience here or was there another motivation for working here? Also, did you enjoy going to school here as much as you like teaching here? Thank you for your time! Dbashour (talk) 12:57, 5 September 2017 (PDT)
The alma mater factor certainly helped, plus the notion of coming back to now work with a lot of former professors as colleagues. However, a major factor as well was the shift in emphasis toward more teaching. I came to LMU from a position at UCLA that was entirely research-driven—as in, if you don’t get a grant to fund you, then your salary is at stake! Ultimately not as satisfying. Research is a part of the academic endeavor, but I preferred to have more teaching in the mix…and a more stable livelihood to boot.
As for going to school here, yes, I must say that felt too short. I had a major blast in college and wouldn’t have minded staying longer if I weren’t obligated to move on with my life, haha!
Hi Dr. Dondi! Seeing as how you're in Computer Science, and it's typical that many of us enjoy science fiction: What is your favorite Sci-Fi movie and why? ArashLari (talk) 14:48, 5 September 2017 (PDT)
Hm, very hard to pick a sci-fi movie favorite…there have certainly been good ones but none I think that have reached the level of my favorite science fiction books. Blade Runner is up there, as are 2001 and The Matrix. I would have liked to have seen better adaptations of Dune, Ender’s Game, and Hitchhiker’s Guide to the Galaxy; Childhood’s End was not bad though that was more of a limited series and not a film. Finally, one of my favorite science fiction works has not yet been adapted into a film: the Foundation series by Isaac Asimov. That would be great to see, but I realize that it would be hard to do well as a film.
Hi Dr Dondi! As a Batman fan, and presumably a DC fan, did you get the chance to see Wonder Woman? If you did, what did you think of it? Nicolekalcic (talk) 22:09, 6 September 2017 (PDT)
I enjoyed Wonder Woman a lot, and certainly agree that it deserves all of the acclaim that it has gotten. It works on every level, and has significant behind-the-scenes milestones as well. Plus, its message and heroine have turned out to be unexpectedly timely. It most certainly sets a high bar for future films in the genre!
Contents
Week 9 Lifeline Q&A
John Lopez
Question
Hello! I would like to spend my lifeline clarifying what data we are supposed to return.
So using the command I have developed, the following comes up when I intend to search for BRO1.
{"results":[ {"symbol":"BRO1","length":2535,"scoreType":null,"description":"Cytoplasmic class E vacuolar protein sorting (VPS) factor; coordinates deubiquitination in the multivesicular body (MVB) pathway by recruiting Doa4p to endosomes","jasparAccession":null,"primaryIdentifier":"S000006005","cytoLocation":null,"score":null,"jasparFamily":null,"sgdAlias":"LPF2 ASI6 NPI3 VPS31","qualifier":"Verified","functionSummary":null,"phenotypeSummary":null,"featureType":"ORF","name":"BCK1-like Resistance to Osmotic shock","featAttribute":null,"secondaryIdentifier":"YPL084W","id":1015987,"jasparClass":null,"briefDescription":"Cytoplasmic class E vacuolar protein sorting (VPS) factor","status":"Active"}, {"symbol":"BRO1","length":null,"scoreType":null,"description":null,"jasparAccession":null,"primaryIdentifier":"orf19.1670","cytoLocation":null,"score":null,"jasparFamily":null,"sgdAlias":"orf19.9239 IPF25590.1 IPF8087.2 Contig4-3069_0020 orf6.5745 CA3475 CaO19.9239 CaO19.1670","qualifier":null,"functionSummary":null,"phenotypeSummary":null,"featureType":null,"name":null,"featAttribute":null,"secondaryIdentifier":null,"id":66043773,"jasparClass":null,"briefDescription":"Class E vacuolar protein sorting factor; role in transport from multivesicular body to vacuole; not involved in Rim101 pathway; macrophage and pseudohyphal-repressed; flow model biofilm induced","status":null} ],"executionTime":"2017.10.30 15:58::21","wasSuccessful":true,"error":null,"statusCode":200}
Out of the two objects given in the results array, which one of these two are we supposed to return for the final product?
Answer
On a general level, you want to choose the record that looks like the definitive one, the one with the most complete information. If you examine the two records, you will notice that the second one has a lot more nulls than the first. This inclines us to choose the first record, but we also want something more, shall we say, computable because eventually a machine will be making this choice.
So, after examining the two records, we observe that in the first record, we have a primaryIdentifier whose value is S000006005—this is how IDs look in SGD. The second record has a primaryIdentifier of orf19.1670 which, though it might have some validity, does not align with the ID system used by SGD. On that note, I'd say that we want to go with the record whose primaryIdentifier matches the pattern of an SGD ID.
Hope that answers your lifeline question!
—Dondi (talk) 21:11, 30 October 2017 (PDT)
Simon & Dina
Question
Hey Dondi! this is the official lifeline from Dina/Simon being cashed in (Dina said I could use it for IxD purposes if that okay with you haha!)
Im using:
searchButton.click(() =>
$.getJSON("https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene", {
symbol: searchTerm.val()
}).done(results => searchResultContainer.empty())
);
Should this not return all the data related to the Gene symbol that is entered by the user (i.e "searchTerm.val()")?
I don't know what it is and I'm sure its something small but I just cant get any info to go into my html page.
I know for a fact that the:
curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=SPT15
Returns:
{"results":[
{"symbol":"SPT15","length":723,"scoreType":null,"description":"TATA-binding protein (TBP); general transcription factor that interacts with other factors to form the preinitiation complex
at promoters; essential for viability, highly conserved; yeast gene can complement mutations in human homolog
TBP","jasparAccession":"MA0386.1","primaryIdentifier":"S000000950","cytoLocation":null,"score":null,"jasparFamily":"TATA-binding","sgdAlias":"TATA-binding protein TBP TBP1
BTF1","qualifier":"Verified","functionSummary":"DNA- and chromatin-binding general transcription factor that recruits other transcription factors in preinitiation complex assembly for RNA
polymerases II and III, and rDNA transcription by RNA polymerase I; subunit of TFIID and TFIIIB; also involved in the chromosomal incorporation of transposable
elements|uniprot_proteome=UP000002311","phenotypeSummary":"Essential gene; conditional mutants grow slowly, are sensitive to heat and DNA-damaging agent MMS; some mutations
increase ethanol tolerance; heterozygous diploid null is haploinsufficient; overexpression interferes with silencing","featureType":"ORF","name":"SuPpressor of Ty
insertions","featAttribute":null,"secondaryIdentifier":"YER148W","id":1009998,"jasparClass":"Beta-sheet","briefDescription":"TATA-binding protein (TBP)","status":"Active"}
],"executionTime":"2017.10.30 16:00::46","wasSuccessful":true,"error":null,"statusCode":200}
So why is it that I cant get the information from the query's return in my html page?
HELP ME SEMPAI!!!!
Simonwro120 (talk) 16:32, 30 October 2017 (PDT)
Answer
Greetings,
First off, I should clarify that you are not expected to write code for this assignment. What you did in curl is correct and suffices here. However, since you did specify some code, I will also answer on that level: yes, that code is correct. The code is getting the same data that curl is getting. The issue you are seeing is that the done clause needs to be modified to actually do something with the results parameter. For example:
$.getJSON("https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene", {
symbol: "SPT15"
}).done(results => console.log(results));
Note how we have changed the done function to results => console.log(results). This will display the results data on the console. If you execute this, you should see the same data that you are seeing via curl.
The underlying principle here is: if you are trying to adapt someone else’s code, make sure you are clear on what the entire piece of code does. The original function that was in there, results => searchResultContainer.empty(), does nothing to display your results. In fact, it doesn't do anything to the data; it just empties out whatever elements are in the searchResultContainer variable. Modifying it even to a simple console.log shows you that you were indeed doing the right thing.
The other way that you could have assured yourself that the code was correct was by looking in the Network tab of the browser developer tools. With that tab open, you would have seen your request go out, and you would then have seen the incoming response as being the same one you saw in curl.
Hope that answers your lifeline question.
