Wikipedia talk:USEP/Courses/JHU MolBio Ogg 2013/Group 81D

Article Selection Discussion
Hi Tisquestra! Have you given any thought to any articles that interest you? The selection is wide and so I was curious if your own expertise might contribute to our selection. As I was browsing, I considered the fluorescent tag article. It has a lot of potential for information, images, etc. The same goes for the immunolabeling article. These are just my suggestions but I am open to any preference you have.Jberendt (talk) 12:32, 2 March 2013 (UTC)
 * Hey Jamie! I took a list at the articles available for us, as well as the two you just mentioned. For me personally, I have two requirements for editing an article: I should feel it has to have enough material to research on that would give us concrete varied examples and topics to write about (keyword being varied), and I should be interested in learning more about the subject (our contributions are going to be available to the public after all!). Keeping both of these in mind, I would choose the fluorescent tag article from the two that you mentioned. The article currently only has a few sentences and would benefit greatly from improvement. From the full list of articles that were given to us, I also saw the gene map and RNA silencing articles that interested me. We've learned a bit about both of these for me to understand what kind of research we would need to do (I think).


 * So...what do you think? I'm totally open to more discussion until we iron out something we both feel comfortable editing. Tisquestra (talk) 06:38, 4 March 2013 (UTC)


 * Tisquestra, I agree with your criteria. All 3 articles (fluorescent tag, gene map, and  RNA silencing) are all similar in the amount the article lacks.  I think we could find a lot of information on any of these.  Are you leaning towards one in particular?  I'm sure we will learn a lot about any of these topics as we get into it.  I was thinking about the different topics and subtopics we could find on the article about fluorescent tags and I came up with ideas about background/discovery, chemical nature, how it works, how it is used, kinds of research it aids, etc.  I was also thinking that this article could have a lot of beautiful images that would help its appearance.  What do you think?  I need to check if other groups are considering this one as well.Jberendt (talk) 02:40, 5 March 2013 (UTC)


 * FYI: Group A did an assessment on the fluorescent tag article so I posted on their talk page to ask if they were considering this article as well.  Jberendt (talk) 11:03, 5 March 2013 (UTC)


 * Hey Jamie, I really like your methodical approach. I went back to the two articles I mentioned to try to do the same. I noticed that  RNA silencing has been linked to RNA interference as being a significant contributor to silencing. That article happens to actually be a lot more thorough, so I'm wondering if the topic of RNA silencing has as much scope for us to dwell into.
 * I tried to think about what we could write for the gene map article. I would see us going into recombination frequency and the breakdown of the genome into intergenic DNA, introns/exons, etc, and explain how recombination affects the distance in a gene map. It makes your approach to fluorescent tagging sound way more interesting =). Also, I was realizing that this masters program is really great, but since it's online, we won't get too much in-depth knowledge of practical lab concepts, which I would really like to understand. The fluorescent tagging article would be great from that standpoint.


 * In short, I'm totally ok with the fluorescent tag article and I say we go for it. I noticed that some groups have just claimed their article, even while they're still trying to see if there are any conflicts with other groups. I've done the same. Let me know if any other group disagrees, and we can see about using gene mapping as our backup.Tisquestra (talk) —Preceding undated comment added 01:38, 6 March 2013 (UTC)


 * I see we have fluorescent tag assigned as our article! This is great!  I have not seen any response from Group A on their talk page so hopefully we are in the clear.  I think we will enjoy this topic very much.  Thank you for editing the page.  We can now move forward with our summary of choice.  Do you have a preferred method to tackle these kind of assignments now and in the future where we are supposed to post from the both of us?  Just from experience with online group projects, I have found it to work well to divide it up and proofread/edit each other.  In a case of a smaller writing assignment, one can start with a rough draft and the other come in and modify and add to it.  I don't mind starting with a rough draft if you wouldn't mind adding to it or editing.  Talk to you soon!  Jberendt (talk) 02:59, 6 March 2013 (UTC)


 * Hey Jamie, great paragraph, thanks for taking it up =). I modified it just the slightest, and I think we're good to go now for this assignment! Good job! Tisquestra (talk) 21:48, 6 March 2013 (UTC)


 * Tisquestra, I was concerned about the length of our paragraph. I have a word count under 200 so far when it needs to be between 200 and 300.  I started drawing a blank last night but it was late and so I thought I would add more if possible today.  If you can think of anything else to add, let me know!  It is pretty descriptive as it is so Dr. Ogg might see it as ok, but still I thought we would try to add a little more.Jberendt (talk) 18:59, 6 March 2013 (UTC)


 * Hey Jamie, yes you are right, I didn't realize that when reading the paragraph (it seemed to display the right amount of information to me). I went back over and tried to enunciate what we were trying to do with the article in a clearer way. Also, I looked at other groups' articles and I realized most were giving a little bit more depth of why the article needed their improvement, so I tried to add that to our paragraph as well. When I was done editing, the total count came down to about 230 words, so I think we're fine now. Feel free to take a look over that paragraph and asses whether or not my sentences make sense =). Thanks! Tisquestra (talk) 21:48, 6 March 2013 (UTC)


 * I like the organized approach! Great job!  I think this will do for our assignment this week!  This will lead nicely into this coming unit's assignment with our outline as it appears we are already thinking of this in the summary.  Thanks! Jberendt (talk) 02:57, 7 March 2013 (UTC)

Immunolabeling
Hello, Jamie and Tisquestra! I see that you two are leaning more towards the fluorescent tag article; however, I noticed that you mention immunolabeling as a potential article for your group. Our group (group B) had some interest in the immunolabeling article, but we wanted to run it by your group before we made our final selection (if we decide to do immunolabeling). Thanks! Jbmontgomery24 (talk) 19:26, 5 March 2013 (UTC)
 * Hi JB! (can I call you that?)
 * Thanks for checking with us. I believe at this point we're actually trying to figure out our article from our other three choices. Immunolabeling is not near the top of our choices, so if you would like to choose that as your article, I think that is ok for our group. Tisquestra (talk) 00:57, 6 March 2013 (UTC)


 * Sure! Jessica or JB is fine.  Not a problem.  We made the selection just a little while ago, but we didn't think it would conflict with your group since you had other front runners.  Best of luck with your article choice!  Cheers! Jbmontgomery24 (talk) 01:33, 6 March 2013 (UTC)

Getting started: Unit 7
I was glancing over the milestones for this week and it seems we will have a lot of research to do so I would like to get started. Do you want to plan on using your sandbox? I don't care either way! Jberendt (talk) 03:15, 7 March 2013 (UTC)
 * Oops, just saw this. I already wrote on your page saying the same thing =). Yea, I'm looking at some articles today that can help us get started. I'll post them on this group page. Feel free to add onto my outline until we have something we're satisfied with!


 * Edit:I mainly gathered several sources to start up this outline. I will be going back through the sources and make more sense of them to gather more details to add later. Tisquestra (talk) 07:49, 9 March 2013 (UTC)

Fluorescent Tagging article outline

 * The different kinds of methods and types of tagging used (where it stands today)
 * isotope markers, or radioactive tracers
 * colorimetric biosensors
 * a thermistor is placed at the beginning of a reaction and end, and the enthalpy change is measured. the environment and reaction is sufficiently small that a large percentage of the heat can be assumed to directly relate to the reaction alone.
 * photoswitchable, which is a type of photochromic compound
 * An example : reversible photoswitchable fluorescent proteins
 * another example : PS-CFP2 and Dendra2 are fluorescent before photoactivation, but switch to red after photoactivation
 * biomaterials
 * electrochemical sensors
 * fluorescent labels
 * extra-sensitivity and non-destructivity makes this the best option for tagging
 * example: synthetic fluorescent proteins
 * GFP proteins used to determine proteins of interest
 * use metal-chelation and fluorophore metal complexes
 * When fluorescent tagging would be useful vs other methods
 * helpful for visualizing function and conditions of molecules
 * The chemistry behind fluorescent tagging, and how it differs by method, including common sources one would use to perform this technique in the lab
 * Famous people that have made breakthroughs with respect to this technology
 * The history of fluorescent tagging and how it was invented
 * Radiotopic labeling used, but not very safe (radioactive effected molecule that needed to be observed itself) . Then fluorescent tagging was discovered

Also:

-> as a note, there exists an article already that I noticed, called fluorescent labelling, that's kind of a synonym of fluorescent tagging. It also has extremely minimal citations, etc but it does have a little more information. Perhaps we can link it to our article.

-> I found a really good pdf of basic fluorescent tagging methods, which I've already cited in the outline above (ref 3). If you want to read and give further details, here is the pdf.

Tisquestra (talk) 09:19, 9 March 2013 (UTC)


 * Tisquestra, thank you for getting this started. I have copied the outline and sources and put them in my sandbox.  So if you want to change or add anything, do it there so we keep it most up to date.  I took a look at the article you suggested above but I assume you mean your reference #1 since that is where your link took me.  It was a good overview and I agree it will be very helpful.  We may want to consider adding a little about each of the different labeling types it goes over: chemical, enzymatic, protein, and genetic labeling .  I will update the outline as I see fit and let me know what you think here.  I also have some texts I want to add that I think have a lot of useful information.  You may have them as well since they are text books for Biochemistry and Advanced Cell Biology. There some great method descriptions written in these texts, might as well utilize them!  Also, have you started looking for images? I have found several in the Wikimedia Commons for the Fluorescent Microscope Images category.  We just need to link which ones will be relevant to our topics in the article.  Talk to you soon!  Jberendt (talk) 03:00, 11 March 2013 (UTC)


 * After pasting the outline in my sandbox and making my additions and edits, I can't get the references to list at the bottom. You will notice the two that are there are my two from one of the previous assignments.  I am assuming that maybe we can't have more than one reflist on a page???  Do you know?  If not I will ask an OA.  Or maybe I accidentally edited the citations but I doubt it since they all do not work now.  Not sure what to do if we can't have more than one reflist unless I can delete the previous assignment.  Again, a question for an OA.  Jberendt (talk) 04:17, 11 March 2013 (UTC)
 * Hey Jamie, I agree, it was a bit confusing. There was an error message on the bottom of the page that had a help page that I used. Apparently, if you have multiple reflists, you have to close them in order to have the citations match up. I think it was because of that that it was getting confused. Anyway, I've fixed it now and we have all our references set up. I'll continue editing on your page. I've been editing what I can on a nightly basis mostly. Since you're editing it now too, you want to split it up? I had started looking into examples of each of the labeling types from the Sahoo reference, so I can continue looking into that. I have not focused on gathering pictures, but you bring up an excellent point. I'll be on the lookout for whatever looks good for the examples I'm trying to find. Should we just include the image itself in our outline? Or do we just leave it as a reference for now?Tisquestra (talk) 06:12, 11 March 2013 (UTC)
 * Oh good, I'm glad you were able to find how to fix that! Didn't see the help page down there, I'll be sure to pay closer attention!  We can definitely start to split things up, especially since we will want to do this for our first contribution.  As far as this unit goes, I think we have a great rough draft outline.  I think we only need to weed out maybe what we can't find good sources on or not much information on and just clean it up a little for a good flow to the article.  I will continue to look at images. I believe our instructions say to make a list so that's kind of what I started.  I will try to find more background sources and sources about present day discoveries using fluorescent tags.  Question: I noticed the bullet points for biomaterials and electrochemical sensors.  Did you have something in mind for these?  Sources?  Not sure where you came up with these for topics. . .just so I am on the same page!  Then we just need to post on our article talk page what we need intend to do to improve the article and I believe we are set! Jberendt (talk) 01:47, 12 March 2013 (UTC)
 * Hey Jamie, yea sorry I'll cite the reference - I saw the electrochemical and biomaterials tagging as part of the Sahoo article. Yea sure, I can look into them and add my list of images as well. The outline does look nice. Good work! For the article talk page, when we mention the improvements we want to make, should we just mention this outline?Tisquestra (talk) 13:50, 12 March 2013 (UTC)
 * I think we should hit the main points of our outline. It might be easiest to read and understand what we intend to do by writing a short paragraph stating that we are planning to improve the article as part of our class project and then make bullet points of our main topics.  What do you think?  Jberendt (talk) 19:56, 12 March 2013 (UTC)


 * Maybe something along the lines of:
 * This article has been selected for improvement to complete a class project for the Johns Hopkins University 410.602 Molecular Biology Course. Main topics for construction include the following:
 * History of Fluorescent tagging
 * Methods and types of tagging
 * Fluorescent labeling techniques and chemistry
 * Latest discoveries utilizing fluorescent tags
 * Advantages and disadvantages


 * These topics will be expanded upon based on reliable sources, and images will also be utilized to improve the quality of this article.
 * How does this sound to you? Feel free to edit! Jberendt (talk) 03:01, 13 March 2013 (UTC)


 * That looks very clear and concise, looks good! Did we want to mention briefly alternate technologies to fluorescent tagging, and why fluorescent tagging has an advantage/disadvantage over them? I'll go ahead and put this outline on the article's talk page and we can edit it thereTisquestra (talk) 17:21, 13 March 2013 (UTC)


 * Sure, I was trying to word something along those lines but realized I was trying to convey advantages/disadvantages so I just left the bullet point as just that. But if we add alternate technologies, we may need to expand our research, which is fine.  I think for now what we have is fine.  We can always add it later as we get into writing and more research to see if that is something we want to do. Thanks for posting it to the article! Jberendt (talk) 22:26, 13 March 2013 (UTC)

Trouble with RSC articles
Hi Tisquestra! I have had some trouble lately getting any articles from RSC to open. Particularly, the Sahoo et al. which we have referenced many times in our outline. I was wondering if you were having any troubles as well, or if I have a computer issue. Basically the page never loads and times out on me every time. Thanks!!Jberendt (talk) 02:27, 29 March 2013 (UTC)
 * Hey Jamei! I think I had to create a few user login when I wanted to look at the full text of this article. Clicking on the link in our reflist brings up the login page, but a user can still access the free material. Did you have any trouble along those lines? Tisquestra (talk) 02:40, 29 March 2013 (UTC)
 * Not sure. I put in my user name and password (for accessing any RSC article) and the page becomes unresponsive.  Since it seems you are not having the same issue I believe it has something to do with my computer and I may have to do some maintenance.  I just thought it was strange that it only occurs on the RSC login page.  Hopefully I can get this resolved quickly!  Thanks! Jberendt (talk) 10:18, 30 March 2013 (UTC)
 * No worries! I got it figured out finally!  Just needed some upgrades and much needed maintenance! Jberendt (talk) 02:55, 2 April 2013 (UTC)

Contributions

 * By the way, I see that the fluorescent tag article is coming along nicely. Sorry I've been a little MIA, I plan to work on some of it tonight since we have a deadline for this unit. Then perhaps we can discuss any points that we might be stuck on tomorrow and the day after? Does that sound ok to you?Tisquestra (talk) 20:33, 2 April 2013 (UTC)
 * Sure! I will be working on it tonight and tomorrow. . .plus we need to remember to post our update!  See you on the article page!Jberendt (talk) 01:46, 4 April 2013 (UTC)
 * Just to touch base, so far, all of my contributions have been prose (as she states in our outline). . .adding content, uploading images, etc. Have you done anything that isn't obvious that we will want to mention in our post tomorrow?  Thanks!Jberendt (talk) 04:11, 4 April 2013 (UTC)


 * I've also been adding prose to the article as well. On that note, I actually have a few images I'd like to add but I noticed that we might have too many images going on in our article and they're all getting staggered in locations that are not relevant to their topic. I didn't want to go around erasing the images you've put up, but do you see any images that might be redundant that you think we may not actually need? Or perhaps we should make some of the images smaller, if we can do so without losing granularity. Tisquestra (talk) 06:46, 4 April 2013 (UTC)


 * I noticed too that they are off, and were worse before we had more content. I was hoping as we added more and more they wouldn't be so out of place since the article will grow in length.  Of course, we can remove them, but we may find that it turns out ok once we have all our content in there.  Do you want to wait or add them back in later to see if they look better?  We might want to continue this discussion on the article talk page so editors can give their opinions if they want. Jberendt (talk) 19:17, 4 April 2013 (UTC)
 * Cool, thanks I'll respond on the talk page as well. By the way, do you know how much progress is necessary for this round of editing on our article? I've been slowly adding to the methods, but each one takes a lot of research to come to a general understanding and be able to say anything in laymen's terms. Do you know if we should have all of our sections filled in?Tisquestra (talk) 02:37, 5 April 2013 (UTC)
 * Judging by the Outline, this is a work in progress in which we were supposed to get a good start on it. I don't believe we needed to have all sections filled just for this Unit.  We got a good start and fulfilled the 8-10 paragraphs requirement.  I agree that it definitely takes a lot of time to understand and summarize each section!Jberendt (talk) 03:20, 6 April 2013 (UTC)

Biomaterials
Tisquestra, I am having trouble deciphering our section on biomaterials and I am wondering if this was a misconception on our part. I think that the biomaterials we added in our outline is actually part of the photoswitchable biomaterials or photochromic compounds in this case. We just somehow made it a new topic? Am I missing something here? If you think we shouldn't have made this a topic and is actually part of the photochromic compounds we can modify accordingly. Thanks!Jberendt (talk) 05:05, 25 April 2013 (UTC)
 * Jamie, I've edited the biomaterials section, and I do believe it is different than the others. Would you still consider it as part of the photochromic compounds?

On a side note, I realized that all my watched pages are no longer sending me emails for some reason, other than the main fluorescent article talk page. I noticed several comments made elsewhere and I'm just now getting to them =(. Hopefully I haven't missed anything!Tisquestra (talk) 03:54, 26 April 2013 (UTC)


 * I see you added to this topic and it sounds good to me. Oh, just what you need!  I figured you were just really busy but I don't think you have missed too much.  Just some responses to our reviewers.  To get to Klortho's critique: what do you suggest about fixing our confusion of terms "tagging" and "labeling"?  The way I think of it is basically you "label with a tag" and so "tagging" would essentially be the same as "labeling".  Am I correct in my thought process?  I will research this some more, but what are your thoughts on it?  Have a good night! Jberendt (talk)  —Preceding undated comment added 04:03, 26 April 2013 (UTC)
 * Jamie, thanks for letting me know. Yea I went manually through my "watchlist" page on wikipedia and saw what I had missed. If I notice it continuing I might have to talk to Klortho about it. (right? he's the person we talk to?).


 * I responded to the section on the article's talk page about the labeling vs tagging terminology as best as I understood. My explanation was different than what you say, so now I'm rather confused. But since it seems that is a mutual feeling, perhaps it is best then for us to take this review week to see what details we can find that might help to clarify our usage of these two terminologies.Tisquestra (talk) 08:21, 26 April 2013 (UTC)
 * After reading your response, I see where we are both describing tagging vs labeling similarly, yours is just more technical. But I think we should definitely somehow clarify.  A simple statement in the lead of labeling vs tagging might take care of the issue and then we can modify anywhere that is particularly confusing.  Let's see what Klortho responds to your suggestion first.  Thanks!  And yes, I would ask Klortho about your email issue.  Frankly, since I don't always check my email regularly, I just frequently check my watchlist.  I should check up to see what is going on with mine as well. Jberendt (talk) 14:18, 26 April 2013 (UTC)

Final Contributions
Hi Tisquestra, hope you are finding your last week eventful in wrapping things up for the semester. How do you want to tackle our final edits? We have a few things to weed out especially pertaining to the "tag" vs "label" issue. There are also a few other things that our reviewers pointed out. Just thought I would touch base with you to see what your schedule was like this week and begin wrapping up this project. I plan to devote most of my time to this project Tuesday - Thursday so I can get most of everything else out of the way first. Talk to you soon!Jberendt (talk) 20:19, 6 May 2013 (UTC)
 * I will work on the last two sections since I started those and take the suggestion of adding content about the Halo Tag possibly if I see it fits. What do you think about Nguych01's suggestions on editing the Methods and types of tags header to "Methods of visualizing biomolecules".  I like it and think this actually clears up the confusion quite a bit!  And as far as our "tag" vs "label" issue. . .what do you think about explaining tagging and labeling in the lead so we can leave the headers and terminology as is?  Jberendt (talk) 01:58, 8 May 2013 (UTC)
 * I have gone ahead and made a few changes as you will see what I mention on the article talk page. It can always be changed back if you don't agree. . .mainly the lead and some header names.  Jberendt (talk) 03:38, 8 May 2013 (UTC)
 * I have made some modifications and reworded areas in the lead and history to hopefully make things more clear. See what you think and let me know if you agree.  I, for the most part, have hit all of our critiques other than the photochromic compounds section and also a response to how the isotope and electrochemical sensors relate to our article.  My thought is that these are necessary since they are an alternative to fluorescent tagging but wanted your agreement on that first.Jberendt (talk) 18:15, 8 May 2013 (UTC)
 * Hi Jamie, thanks for making the edits that you mentioned. I have also gone through and tried to clarify what I could of the labeling vs tagging terminology. I edited the photochromic compound section as well. I do agree that isotope and electrochemical sensor sections should still remain in the article, but perhaps I should try to explain how they tie into fluorescent tagging. I will make those edits shortly. I'll also take a look at the history section that you edited as well.
 * Since you've taken charge and done the other reports in the past, I thought I'd go ahead and write up the final progress report. Prof Ogg wanted it to be short so I've put it up on our group page. I thought it would be best if we simply outlined the total contributions we've made to the article, and as I remember, we started with something pretty barebones so all the sections other than the introduction are things we've put in. Feel free to edit the outline further.Tisquestra (talk) 21:22, 9 May 2013 (UTC)
 * Looks great, thanks! I only added the contributions I used from our reviewers.  I read through the photochromic section and I think it reads much better.  Over all, I feel pretty comfortable with our article for this project.  Congrats on the end of the semester and a close to the project!  If we don't communicate any further, good luck with the rest of your courses.   Maybe we will work together again in the future.  It was a pleasure!  Jberendt (talk) 22:11, 9 May 2013 (UTC)
 * Awesome! I made a few more changes. I like the edits you made to the progress report as well. I think we're good to go! It was definitely a pleasure working with you Jamie, I hope we run into each other in this program soon!Tisquestra (talk) 00:43, 10 May 2013 (UTC)