I'm gonna pay $1350 for this? Come on PLoS ONE!

From: Jan Halborg Jensen [jhjensen@chem.ku.dk]
Sent: 7/18/2012
To: xxx@plos.org
Subject: Author Query to Editor PONE-D_12-07445R1

Hi,

Is there any news regarding this manuscript?  It has been close to 6 weeks now.

Best regards, Jan

---------

On Jul 18, 2012, at 10:30 AM, plosone wrote:

Dear Dr. Jensen,

Thank you for contacting PLoS ONE.

I can confirm the reviews have been submitted and your manuscript is currently with the Academic Editor for a decision, as soon as the decision has been completed we will be in contact.

Kind Regards,

xxx
EO Staff
PLoS ONE

----------

From: xxx
Sent: Wednesday, July 18, 2012 5:54 PM
To: Jan Halborg Jensen
Subject: Re: Author Query to Editor PONE-D_12-07445R1

Dear Dr. Jensen:

The paper is still under review. 

Sincerely, 

xxx - Editor, PlosONE

--------

From: Jan Halborg Jensen [jhjensen@chem.ku.dk]
Sent: 7/19/2012 1:47 AM
To: xxx@plos.org
Subject: Re: Case: 01158374    [ ref:_00DU0Ifis._500U04XUWc:ref ]

Thank you, but I got the following email from the editor.  I am a little confused.

Dear Dr. Jensen:

The paper is still under review.

Sincerely,

xxx - Editor, PlosONE

----------


Sent: Tuesday, July 24, 2012 2:51 PM
To: Jan Halborg Jensen
Subject: Re: Case: 01158374    [ ref:_00DU0Ifis._500U04XUWc:ref ]

Dear Dr. Jensen,

Thank you for contacting PLoS ONE. 

Please accept my apologies for any confusion caused by my previous email. In regards to your manuscript PONE-D-12-07445R1, I can confirm that the comments from two reviewers have been submitted. We are in contact with the Academic Editor who will soon be able to make a decision regarding your manuscript and inform you of his decision. 

Please do not hesitate to contact me if you have any further questions or concerns. 

Kind regards, 

xxx
PLoS ONE Staff

--------

Update



Sent: Thursday, August 02, 2012 5:11 PM
To: Jan Halborg Jensen
Subject: Status update for your submission to PLoS ONE: PONE-D-12-07445R1 [A Computational Methodology to Screen Activities of Enzyme Variants]

PONE-D-12-07445R1
A Computational Methodology to Screen Activities of Enzyme Variants
PLOS ONE

Dear Dr. Jensen,

I would like to take this opportunity to update you with regards to the current status of your manuscript as we are aware that it is taking longer than we anticipated for you to hear back from the peer review process of your submission.

Please accept my most sincere apologies for the delays you have experienced during the peer review process of your submission; whilst reviews have been received the Academic Editor would like to consult further in order to reach a decision.

Please rest assured that it is receiving our full and urgent attention. I know that this can be a frustrating process, but if I can ask for your continued patience whilst we are attempting a speedy resolution.

We appreciate your patience, and hope you will contact us if you have any questions or queries.

Regards,

xxx
Staff EO Lead
PLOS ONE

-------
Update 2

From: Jan Halborg Jensen [jhjensen@chem.ku.dk]

Sent: 8/27/2012

To: plosone@plos.org

Subject: Author Query to Editor PONE-D-12-07445R1

Manuscript information:

========================

PONE-D-12-07445R1

A Computational Methodology to Screen Activities of Enzyme Variants

PLos ONE

========================

Dear Editor

Is there any news regarding this submission.  If not, when can I expect to hear something?

Best regards, Jan

-----

From: xxx

Date: August 28, 2012 1:04:59 PM GMT+02:00

To: Jan Halborg Jensen <jhjensen@chem.ku.dk>

Subject: Re: Author Query to Editor PONE-D-12-07445R1

Dear Dr. Jensen,

I apologize for the delay in handling this manuscript.  Your paper is still under review.  You will hear from me within Sept. 15, 2012.

regards

xxxx

Associated Editor, PlosONE

------

From: no-reply@salesforce.com [no-reply@salesforce.com] on behalf of plosone [plosone@plos.org]

Sent: Wednesday, August 29, 2012 11:10 PM

To: Jan Halborg Jensen

Subject: "Author Query to Editor PONE-D-12-07445R1"  ref:_00DU0Ifis._500U04r2d9:ref

Dear Dr. Jensen,

Thank you for contacting PLOS ONE.

I can confirm that your manuscript is currently out for peer review. We are in contact with the Academic Editor and are working to ensure that the review continues to run smoothly. Please do not hesitate to contact us again if we may be of further assistance.

Kind Regards,

xxxxx

--------

From: Jan Halborg Jensen
Sent: Monday, September 17, 2012 1:49 PM
To: xxx
Subject: Re: Author Query to Editor PONE-D-12-07445R1

Dear xxx

What is your decision regarding our manuscript?

Best regards, Jan

----

From: xxx
Sent: Monday, September 17, 2012 4:28 PM
To: Jan Halborg Jensen
Subject: Re: Author Query to Editor PONE-D-12-07445R1

Dear Jan

thanks for  your message. I still need few days more to get the last referee report and then I will get back to you.

Regards

xxx

----

The reviews arrived on September 24th.  You can read the rest here.  Tl;dr: the paper is now accepted

First PLoS ONE article published!

It has taken a little more than a month to get it from accepted to published. There were a few issues which was related to the supporting information which must be included in the manuscript and not separately in the final form (but not required when you submit it for review).

Anyways, give it a read if you feel like it: http://dx.plos.org/10.1371/journal.pone.0041117

Now, back to my second PLoS ONE submission and the lengthy review.

BioFET-SIM Instruction Videos

The BioFET-SIM web interface operation is illustrated in 4 short instruction videos:

Basic interface operation

BioFET-SIM signal and pH response calculation

Custom structure upload

Restoring a previous session

Feel free to contact us in case of any questions under
biofetsim at gmail dot com

Using PeerWise to assign homework

PeerWise
This past quarter I used a new tool called PeerWise in a physical chemistry course I co-taught.  The main idea behind PeerWise, which is a free web-based service developed by Paul Denny at the University of Auckland, is that students write multiple choice questions for each other.  I didn't quite have the courage to say "Want homework? Write your own" so instead I used it as a supplement to the normal homework assignments, i.e. I reformulated most of the homework assignments as multiple choice questions and posted them on PeerWise, in addition to the usual homework assignment.

Some information about the course
The course is attended by about 170 chemistry and biochemistry majors and covers thermodynamics and kinetics - more specifically chapters 13-20 in Atkin's Quanta Matter and Change.  It's taught in a 9-week quarter and the students take one other course at the same time.  There are four other faculty members involved who also pick homework problems associated with their lectures.  The students were divided into six teams of roughly 30, and each team has six contact hours with TAs who can help them with the assignments.

Advantages of PeerWise
1. Feedback to the students.  PeerWise allows you to give extensive descriptions (you can even use videos: example 1 and example 2) on how to solve the problem immediately after the student has picked an answer.   The quality of the help provided by the TAs tend to vary greatly, and I hoped this would help even things out a bit.
2. Breaking complex problems up into more manageable pieces.  A standard question usually asks you to compute x given some conditions.  In PeerWise this can be broken up into, for example, a) which of the following equations would you use to compute x? and then b) what is the value x given these conditions.  Answering the first question lets people now whether they are on the right track before proceeding.
3. Feedback to me.  Students can leave questions or comments for each problem, which often helps me improve the explanation or identify errors in the problem.  Students can also rate the quality and difficulty of each question, which is very valuable.  I also get all sorts of detailed data including how many students answered the question correctly (more on that below).

Some data
I put 120 questions up on PeerWise and 119 students answered at least one question.  From what I understand many students worked in pairs and only one would answer on PeerWise.  39 students answered 100 questions or more.  For almost all problems, the majority of students picked the right answer, so they are not just clicking randomly to get the explanation as one could have feared.  For example, for the question with the most (86) answers was answered correctly by 57% while the question voted the hardest was answered correctly by 47% of the 76 students who answered it.

While I encouraged students to write their own questions, only 9 questions were written.  One of these questions was "Do you find PeerWise helpful?"  41 students answered, 38 said yes.  Also several students commented positively on PeerWise with one caveat (see below).

Clearly, many students used PeerWise as a study aid before the exam as seen on this figure.

One main problem: errors
The main complaint by the students was the many errors that crept in to the questions, multiple choice answers, and solutions.  The multiple choice format exacerbates the problem, since many students will work for hours trying to reproduce one of the answers.  This is of course impossible if there is an error and this is very frustrating to the student!

There are several sources of errors.
1. Several errors were introduced by me when I typed in the multiple choice answers (for example, using Joules when I meant kiloJoules) and explanations.
2. Several errors were already in the problems and was copied into PeerWise.
3. Several errors were in the answers provided in the solution manual of the text book and were copied into PeerWise by me.  Often the you would simply get a different numerical answer based on the numbers provided.

The error rate was about 1-2 questions per week and all (hopefully) will be fixed next year.


Tips 
1. By default the questions are listed in the reverse order they are created (i.e. newest one first), so in cases where the order was important I would write the first question last, e.g. exercise 1b and then exercise 1a.
2. Each question comes with a one line preview, so the first sentence in the question should be the name of the exercise, e.g. Exercise 1a.
3. Each question can also be labelled by subject, so I would use labels like "week 1".  With one click one can then display the questions on for a single week only.
4. Many of the comments left by the students said "I punch the solution into my calculator and get a different answer".  It's of course hard to know what the problem is, but in these cases I leave a link to the worked out solution on Wolfram|Alpha (example), which is basically on on-line calculator.
5. You add equation through one of several editors  (I recommend using the Latex editor) that create and image of the equation, which you can't edit. If you view the page in HTML format there is a Latex code you can copy and paste into the editor and change, rather than typing everything in from scratch.

Changes for next year (When was the last time you learned anything by doing it once?)
Overall PeerWise was a hit, and I will use it next year for this course.  I plan to make the following changes:
1. I will add 10-20 math and conceptual training questions every week.  Questions one should be able to answer in 1 second: What is $e^{-0}$?  If $\Delta G^\ominus <1$ what can you say about the equilibrium constant?  Some of these will show up every week! 
2. I will add 1-2 "regular" questions based on topics from previous weeks.
3. I will try to have the explanations include a screenshot of the solution done in Maple.  For three reasons: a) it will make me double check the answer in the solution manual, b) it will remove one source of error if I don't have to retype something, and c) it will encourage the students to use Maple (students who use Maple efficiently are done in a fraction of the time compared to others).

Finally, I am racking my brain on how to get more students to write their own questions.