View source for FAQ Misc

This is a page for miscellaneous FAQs often asked of Jose. 

== How do I edit a page in this Wiki? ==

This is very easy. Just go to this [http://cires.colorado.edu/jimenez-group/wiki/index.php/Test test page]

Then log in (top right corner) and the click the edit tab or the edit buttons to the right. Enter some text and click "preview" or "save" and it'll be there. 

We use the Wiki because it makes posting info on the web extremely easy.

For more detailed help, there is always a link on the left of every wiki page that says "Help", which takes you to the [http://www.mediawiki.org/wiki/Help:Contents MediaWiki help page]

We use the "MediaWiki" software to run the Wiki, so that help is what's relevant. Note that Wikipedia also uses MediaWiki, so once you learn, you can create an entry for something you are interested on in Wikipedia!

== How do I respond to the reviews of a paper? ==

(This is written as a guide for people in our group working on one of their first papers, although it may be of use to others).

In terms of procedure:
* As soon as you get the reviews, please forward them to all coauthors, and ask for any input they may have. This gives them more time and saves a lot of time, if they care strongly about how we respond to some review comment. 
* Then you should work on the revised paper and response document as discussed below
* The revised paper and response document needs to be shared with all coauthors before re-submission. It would be unethical to not share the response document with coauthors, even if the reviews were good and the changes are small. Depending on how extensive the reviews and revisions were and of how many coauthors we have, we may give between a few days and 2 weeks to the coauthors to get back to us. We need to hear from coauthors that they agree to re-submission before we can proceed.

Generally we need to submit three documents in response to the reviews:

*(1) A revised paper 
*(2) A "difference version" of the revised paper, highlighting (e.g. with track changes in Word) all the changes between the submitted and revised versions. For ACPD or AMTD paper, please take care to incorporate all the changes that may have been made at the proof stage.
*(3) A point-by-point reply to all of the reviewer comments. 
** In this document we first copy all the reviewer comments, and number them as R1.1, (reviewer #1, comment #1), R1.2 and so on, in black text. 
** Then we reply below each one, in blue text, as A1.1 (reply to comment #1 of reviewer #1), A1.2, and so on. 
** All changes to the document text need to be given in quotes and in '''bold''' in this document.

Some items to take into account when preparing responses:
* It is good to first create a response document and propose responses to each question, and then share the proposed responses with the key coauthors, before making all the changes in the manuscript. Otherwise time can be wasted by having to change 2 documents several times, before we decide on the final responses. 
* You can read many examples of responses to reviews in the discussion section of ACP and AMT papers.
** However, note that some of the responses are of mediocre quality. We strive for high-quality work, thus it is not OK to copy all practices you may see on those responses.
* Some good examples of good response documents include:
** [http://www.atmos-chem-phys-discuss.net/5/S5775/2006/acpd-5-S5775-2006.pdf This response document of Marr et al., ACPD 2006].
** [http://www.atmos-chem-phys-discuss.net/9/8377/2009/acpd-9-8377-2009-discussion.html The responses in Aiken et al., ACPD 2010].
** (If you see other very well crafted examples, pls link them here or let us know)
* We do not need to implement all the changes requested by the reviewers. Sometimes the reviewers are reading the paper quickly or don't have much background in some sub-area, and thus some comments may reflect a misunderstanding of the manuscript. In these cases it is OK to to disagree with the reviewer, although it is good to ask ourselves: "Could the misunderstanding be caused by our manuscript being unclear? Could the manuscript be made clearer to avoid similar misunderstandings by readers?"

== Why does your group publish so much on ACP? ==

ACP has several key advantages over traditional journals:
* Free open access to papers
* Papers are public BEFORE they are reviewed. In "secret review" journals, nobody knows that the paper even exists until it has been accepted and appears on the web. That represents a delay of typically 4-8 months, sometimes more than a year, in the paper being public, which hurts the visibility of the work and increases the probability of being scooped.
* The reviews and the author responses are public. This is advantageous for at least two reasons:
** The reviews and responses are often very useful to learn quickly what is new, controversial, or well-established etc. about a paper
** The transparency of the publication process is also increased. 
* Non-reviewers can also publish short comments on any paper. This is very useful to receive input from other researchers in the community (even as it creates more work in responding to those extra comments).
* For all of the above reasons, ACP has effectively become the prime journal in Atmospheric Chemistry, surpassing JGR and others in e.g. Impact Factor, Special Issues, etc.

That said, it is always good to publish on a variety of journals as they reach different readerships etc.

== How do you determine whether a paper is "Highly Cited" according to Thomson ISI ==

Thomson ISI publishes thresholds for papers in each field (e.g. Chemistry, Geosciences, or Mech Eng -- this depends on the classification of each journal into fields by ISI) and each year, above which a paper is highly cited. As of Oct-2010, the thresholds are posted [http://www.sciencewatch.com/about/met/thresholds/#tab3 in this page] (although ISI often moves them around). Basically they rank the papers by the number of citations, and they report the number of citations that separates the 1% most cited from the 99% less cited. So e.g. every year we look up the list on the web, and then we compare the citations of our papers with the relevant thresholds for each year of publication and journal field. In our [http://cires.colorado.edu/jimenez/group_pubs.html group publications] page we highlight in '''bold''' all of those papers.

The categories for the journals most relevant to us are:
* Geosciences: JGR, GRL, ACP
* Environment/Ecology: ES&T
* Engineering: AS&T
* Chemistry: Anal. Chem.