Policies Procedures

This page summarizes the policies and procedures of the Jimenez Group at CU-Boulder. The shortcut to it is http://tinyurl.com/PolProc.

Version: 1 Revision: 5 Date: 4-Aug-2013

General Policies & Procedures

Am I expected to apply for fellowships while I am a group member?

Yes, especially for graduate students for which one can apply for fellowships after one has started. We will expect you to take these applications very seriously. In general this is a good idea for several reasons:

• It looks great on your resume
• It gives you independence from funding ups & downs (and protects you from having to TA), and gives more freedom to choose a project or to fine-tune what your research
• It gives you a link with a funding agency which generally opens some doors with them for collaboration and possibly future jobs
• Often you get to meet other fellowship recipients and attend a meeting (sometimes several) sponsored by the funding agency
• If often comes with funding for travel and computers specifically for you.
• It liberates grant money to buy computers, instruments, pay for trips to conferences, etc.

What are the rules for instrument use?

• Each J-Group instrument has a caretaker, as part of everyone's service to the group (see below for more about group service). The list of tasks for each person is kept at http://tinyurl.com/jg-plan, which is reviewed and updated every year during the annual review process. The actual maintenance is tracked via Asana.

• If you use the group instruments, then it is your responsibility to make sure that it's working BEFORE you use it and 100% your responsibility to make sure it's in mint condition AFTER you used it. Any problems you create, you are responsible for fixing.
• Anytime you CHANGE something on an instrument (swap cables, up the MCP setting, add light scattering, upgrade software, etc.) or when a problem develops (even if you think you fixed it) you need to let the instrument caretaker know.

What are the rules for using the shop area on the 4th floor?

All Group members must take a short (less than 30 minute) orientation class with one of the Lab Safety Coordinators as listed in the Jimenez/Ziemann Shop Safety Policy. Please read the policy, and get signed

Can I borrow a _____ from the group for personal use?

• In general the answer is YES for short periods (1 day to 1 week), but pls write it on the clipboard which is attached to the door of the lab BEFORE the item leaves the lab.
• Please return items promptly after you use them (next day).
• For more expensive or critical items please ask the group first via email, and/or ask Jose.

Am I expected to follow the research literature?

• Yes, this is a basic need for someone working in research. It takes time and effort, but there is no excuse for ignorance. Not being aware of recently published research in your field is unprofessional and will give a bad impression to other colleagues at CU, people you meet at conferences etc. and hurt you during your job search after the group.
• You should monitor the key journals within our field for papers related to your research or the group's. These are listed in this link
• You are especially responsible for papers within your research area. You should set up multiple alerts with e.g. Web of Science or similar tools to warn you of papers directly related to your research.
• Each group member is responsible for detailed monitoring of certain journals, and posting and commenting on interesting articles on the Google+ literature community, according to these rules:
  • The list of journals and assigned people is here. People can trade journals etc. by documenting it on that page.
    • Importantly, if you decide to stop monitoring a journal, let Jose know immediately so that we can reorganize to cover all important journals at all times, and drop secondary journals if needed.
  • Feedly is the recommended tool to monitor the literature
  • The number of articles posted per day should be limited to 3 (potentially lower during field studies). If there are 3 posts already, you should wait until the next day. This is to avoid the feed volume becoming too large, which some people find detrimental.
  • Each group member is expected to post at least 1 paper per month, ideally at least 2 per month. The maximum number of posts per person is only limited by the 3 posts per day limit of the feed.
  • The people assigned to a journal have 'exclusive' posting rights for 2 weeks after an article appears. After that time anyone can post older papers from any journal. (Very important papers are excepted). Note that you can add a "tag" in feedly (e.g. named "waiting for posting") to keep such papers until they are openly postable.
  • The detailed format of the posts matters to make it as useful as possible. Figures should be of sufficient resolution, and a sub-figure should be taken if the whole figure will be too difficult to see. The text should have an explanation of why you thought it was useful, either as the title + key text from abstract, or a summary in your own words. Also please use bold by *enclosing in asterisks* to emphasize key idea for rapid reading. Use the "+1" button for posts you find most useful.
  • To post a figure, you need to upload a "photo" which is really a graphic file, JPG, GIF, PNG etc. On a PC you can do one of these: (1) open the HTML version of the paper, for the journals that have that, click on the large version of the figure you want, and just save it in your hard drive. (2) use the "snipping tool" which is part of windows, you can find it on the Start Menu under All Programs --> Accessories. You just drag the cursor around the area that you want to copy, and then save the resulting picture into a JPG. With the snipping tool method it is important to make the graph as big as possible (to have enough resolution) and then you upload into your post as a photo. (3) You can also use the "snapshot tool" in Acrobat to copy a picture into the clipboard, and then you can paste into powerpoint, and right-click on the image and select "save as picture." Again you want to make the figure as large as possible. Note that you should upload the picture into Google+ first, before you paste the link into the text, otherwise it recognizes the link and formats it in a less useful way.
  • Note that comments are only emailed to the person who posted the original post and other people who have commented on that post. If you have a comment that you'd like to share it with everyone, please make it a new post.
  • These rules will be reviewed regularly (every 3 months or so) as the use of the feed evolves and we gain experience

Work Schedule FAQs

• Everyone in the group should work in his/her office and/or in the lab every weekday.
• Working at home is generally discouraged as it often leads to reduced focus and productivity. If you want to work at home some of the time, you need to discuss it with Jose first. If this is approved, you need to enter the times in which you are working at home in the group calendar to facilitate organization of meetings etc.
• Everyone in the group will work in the lab or office for a minimum of 8 hrs which include the period 9:30 am to 4 pm, so that interactions with other group members are possible.
• This still applies if it snows, unless it is a big storm (> 5 inches of snow) or CU is closed.
• Longer hours are typical of research. Typical average work schedules on a research environment like ours are 55-70 hrs a week. Even higher intensity is often critical during field studies and other intensive periods such as before conferences and paper submission.
• For positions which are shared between our group and other groups or companies, a clear accounting of the hours worked for each group is essential for good long-term functioning of the collaborative relationship. This is done via a Google Spreadsheet shared with all parties, which allows for continuous updating and sharing of the information.
  • These timesheets need to be completed by Sunday for the past week.
• Sometimes a group member needs to dedicate work time to tasks which are not part of the group, such as finishing a paper from their PhD, or doing a job search, or writing a proposal for a future job. This is ok, but if these tasks will take longer than 1 day of regular work time, they should be discussed with Jose and marked in the group calendar. Also for postdocs and research scientists, the time should be declared as "vacation" within the CIRES system. That way people still get paid normally, but the time of the non-group work does not get charged to a grant, which would be illegal. Note that if the time involves a paper from a previous group that is collaborative with our group, it is proper group work and this does not apply (but it should still be discussed with Jose for time planning purposes).

What is the format of our group meetings?

• We have tried many different group meeting formats which have various advantages and also sometimes inefficiencies. We will continue to experiment with and are open to suggestions. During very busy periods (field studies, when Jose is teaching etc.) the frequency of group meetings will decrease. As of May 2015 we intend to continue with this system:
  • All-group meetings only for conference presentation rehearsals
  • Separate CIMS and AMS/OFR meetings every few weeks. Time will be limited and allocated to different items. Longer discussions that only concern a few of the people present should be discussed offline.
  • Ad-hod subgroup or one-on-one meetings as needed.
• When calling meetings involving multiple group members try and include those who will benefit from and contribute to the meeting, but also try to be respectful of the demands on people's time.

How do I set up meetings using Google Calendar?

• (1) Events should only be in the group calendar if they involve the whole group (or almost everyone)
• (2) Times when people will be away should be entered as ALL DAY events in the calendar. Sometimes Google Cal will put the event at the actual times you entered (as it recognizes this automatically). In that case people change it to all day event manually.
• (3) Events involving only part of the group should be set up as events in your personal calendar, and then you use the invite function to invite the relevant folks
• (4) If one of the shared conference rooms will be used, you need to do 3 things:
  • (4.1) Check that the room is not already booked at that time by looking at the calendar for jg.labresources@gmail.com
  • (4.2) Start the event name with "CR332: title of meeting" as e.g. for reserving Cristol 332
  • (4.3) Invite jg.labresources@gmail.com as a participant in the meeting, to reserve the room

How frequently can I meet with Jose?

• Jose makes an effort to meet with people as frequently as needed, typically the same day or within a few days of the meeting request at most.
• Group members should not be shy in requesting meetings if needed to discuss research etc., even if Jose appears to be very busy. The same applies to meeting with other group members. Jose will make every effort to meet with you on a timely manner, and will let you know about any delays needed due to current schedule or deadlines.
• At the same time group members should be respectful of Jose's time, e.g. he spends a lot of time reviewing group papers and becomes slower at that important task when there are lots of meetings. So you should always be prepared and organized for meetings.

Can laptops be used during meetings?

• We allow the use of laptops (& smartphones) during most meetings, since often we have to take notes or add tasks to Asana.
• However, in the past group members have complained that excessive laptop use (checking email or doing unrelated work) can make meetings longer and less productive.
• The following policies are proposed (May 2015) to deal with this issue:
  • Laptops should be closed during meetings if possible (except for presenter, designated notetaker, and if searching for papers or other info to inform the current discussion)
  • During meeting breaks, or when the presenter is updating a graph etc., the use of laptops for unrelated items (e.g. email) is allowed. When the break is over anyone can say "laptop rule" to remind others to cease unrelated tasks and close their laptops.

How should I keep a research notebook?

• Everyone doing research is required to keep a notebook, preferably electronic using OneNote.
• You should write on the notebook at the start of each week and each day to briefly summarize what you are going to do and why. You should also paste graphs and discuss results and what may be unclear or needs discussion or further investigation.
• This system will help you think through the problems, discuss them more efficiently with others, and figure out a few months later why you did something a certain why or what you were thinking. If will also help others in the future (when you have left the group and moved on to do other things) to understand what you did and recreate or expand some of your analyses if needed.

Letters of Recommendation FAQs

• Writing letters of recommendation takes time, especially if I have not recently written a letter for you, or if the target audience / position is very different from those of past letters. I request that you respect the following timelines:
  • If I have not written a similar letter for you before, please request the letter 1 MONTH before it is due (via Asana)
  • If I have written a similar letter for you before, please request the letter 2 WEEKS before it is due (via Asana)
  • If there is a hard deadline for the letter, please make it clear in the action step.
  • I always do my best to get letters submitted, but I have sometimes missed deadlines when the requests came with short notices, so please adhere to the above timelines.

Should I get the flu shot every year?

• Yes, this would be greatly appreciated (although it probably can't be strictly required). Besides saving you the possible pain and wasted time of having the flu, you may also save others in the group from contagion, since the vaccine is not 100% effective.

Can I send regular mail or Fedex / UPS etc. for group purposes?

• Regular US mail is not allowed on grants. You can send mail by bringing it to the CIRES message center and stamping it with the CIRES mail code.
• You can send Fedex or UPS as needed and those can be charged to grants. However these are expensive so please be judicious and use them only when needed.

Publication FAQs

What is the group procedure for writing a paper?

• We start with an outline (bulleted abstract + figures), as described in this outstanding paper by Whitesides.
• Once we have agreed on the abstract and the figures, we start the writing of the actual text.

How do we track papers on Asana?

• When we decide to write a paper, we create a task named "Track XX paper to submission", with the appropriate followers. All paper versions and comments should go through this Asana task, to provide a central repository for the discussions that we can find later.
• When the paper is submitted, the above task is marked as complete, and we create a 2nd task named "Track revision of XX paper to publication." The initial task will be very messy by then, and this provides a clean slate at a natural breakpoint. Again all paper versions and comments should go through this Asana task.
• When the paper is published after the proofs are processed, the 2nd task should be marked complete.

What is the group file naming convention?

• File names for ALL non-online (Word, PPT, Excel, PDF etc) files shared within the group and with others should start with the date and be in the format "2013-06-15_LastName_BriefSubject_v1.doc"
  • Date should be on that format with YearIn4Digits-Month--Day. This sorts the files naturally by creation date in Windows etc.
  • Always increment the date & version number in the file name when making ANY changes to the file. Otherwise this can create a lot of confusion and wasted time, and result in losing changes
  • Again, NEVER re-share a file that has had any changes without increasing the version number (it is free!)
  • When reviewing a file and providing any edits or comments, add your initials or name at the end of the file before sharing back, e.g. "2013-06-15_LastName_BriefSubject_v1_Jose.doc"
  • This does not apply to Google Docs since there is only one shared version, but does apply when e.g. making a PDF printout out of a GDoc
  • This may not be doable for e.g. Squirrel or Tofware files, but should be done for all other files of any kind unless there is an important reason why it is not possible

What are the group specifications for outlines to be reviewed by Jose?

___ File names should always follow the group file naming convention above
___ Include your best guess of title, author list, and journal(s) to submit to.
___ Include the key findings as bullets in the abstract.
___ Include only limited / schematic text with section and subsection headings (only if it helps the discussion, otherwise a bulleted abstract may be sufficient).
___ Include all the figures even if incomplete. Write a note below each figures if it needs to be improved, or if the data is not yet fully processed.
___ Include placeholders for missing figures, if possible with a simple cartoon of how the figure may look.
___ Include key literature references that motivate or support the work.

What are the group specifications for papers to be reviewed by Jose?

We spent a lot of effort reviewing and polishing the papers from the group, and some details have to be repeated over and over. Please review and implement all the items below before your paper is reviewed by Jose or others in the group, UNLESS we explicitly agree to a "big picture" review before the paper is complete. (Shortcut to here: http://tinyurl.com/jg-editing)

• General:
  • ___ All group papers will be written in a recent version of Word for windows (Word 2013 or later as of May-2015)
  • ___ File names should always follow the group file naming convention above
  • ___ All sections of the paper need to be there, including abstract, conclusions, figure captions etc., unless we have agreed otherwise beforehand
  • ___ The sections should be ordered as: Title + author list + abstract; introduction; methods; results and discussion (sometimes 2 separate sections); conclusions; appendix (if any); acknowledgements; references; Tables w captions; Figures w captions; Supp. Info.
  • ___ Title + author list + abstract should all be in 1 page
  • ___ Intro, References, Tables, and Figures should start on a new page
  • ___ Page numbers should be in the lower right corner, and line numbering should be continuous
  • ___ Use consistent margins, section title formats, spacings between paragraphs and before and after titles, justification of the text and of the first line in a paragraph etc. across the paper.
  • ___ Please review a few recent papers published in the most likely journal that your paper will be submitted to, and follow other conventions based on that example.
  • ___ Please review the instructions for authors of your chosen journal, such as these for ACP, ES&T, AS&T, or AGU Journals
  • ___ For journals with a length limit (GRL and ES&T) summarize where you are vs the limit on the first page below the affiliations
• General Writing & Expressions
  • ___ Long sentences are more difficult to understand and are prone to misinterpretation. As a rule of thumb, try to avoid sentences with more than 15 words. Break complex ideas into multiple sentences.
  • ___ All acronyms need to be defined on their first occurrence
  • ___ Be aware of your use of acronyms and use them consistently. Reviewers often complain about too many acronyms being used, but acronyms also can save a lot of repetition in the text. Avoid acronyms for terms that are only used very few times in the manuscript, unless they are common ones in our field (e.g. SMPS, PTRMS, AMS, GEOS-Chem)
  • ___ The words "Note that..." or "It is important to note that..." can typically be removed. Use sparingly if really needed.
• Title Page & Abstract
  • ___ Think hard about the title and how to both summarize well your results, and attract the attention of e.g. a reader in Japan who doesn't know about your specific study
  • ___ Include a full author list with affiliations (see previous group papers and/or papers on your target journal for examples)
  • ___ For everyone in our group, the affiliation should be "Department of Chemistry & Biochemistry, and Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado-Boulder." (Except for students affiliated with ATOC).
  • ___ The abstract is the most important piece of the paper, it will be the only item that many people read. If it is important and new, it must be in the abstract
  • ___ Title, author list + affiliations, and abstract should fit on one page if at all possible
• Introduction
  • ___ The introduction should start with the big picture and quickly get specific to the topics of your paper
  • ___ Importantly the context of the previous studies on your specific topic should be summarized, and their limitations that your study overcomes should be pointed out
  • ___ Avoid lengthy descriptions of topics tangential to your paper. We often have to delete entire pages from group draft intros for this reason.
  • ___ A typical introduction is ~2 pages in Word format (~100 lines at Font 12 w/ 1 inch margins). It can be shorter for short papers, but typically not a lot longer.
  • ___ The last paragraph of the introduction should be stand-alone and summarize WHAT you did, NOT summarizing the results
  • ___ A common mistake is to include some site or instrument or model details in the introduction. Those belong in the Methods section. The only place in the intro where you talk about what YOU did is the last paragraph
• Methods
  • For instrument details:
    • ___ For AMS: define HR-ToF-AMS in the methods section, and say "hereinafter AMS for short" (or similar statement) and use AMS only in the rest of the paper (or HR-AMS if we need to emphasize that aspect)
    • ___ Note that the correct use is "PToF" and not other capitalizations.
    • ___ For OFR: refer to it always as "OFR" or "OFR185" or "OFR254". Use "PAM" only in the methods section when describing the actual reactor.
    • ___ For CIMS: define HRToF-CIMS in the methods section, and say "hereinafter CIMS for short" (or similar statement), unless otherwise needed
    • ___ For all other instruments: indicate manufacturer/model or give a reference (see recent group papers to find relevant info)
• Referencing
  • ___ Reference lists need to be complete and properly formatted. It is hard to review papers when the references are incomplete or have many mistakes.
  • ___ We should cite primary references whenever possible. A primary reference is the first one to report a given conclusion conclusively. Sometimes people are lazy and cite a paper that cites a paper that cites the primary reference. This is frowned upon and will hurt you in the long term and serious practitioners that read your papers will quickly realize this lazy practice, so we should avoid it.
  • ___ Check that a reference that you cite for a given point actually provides evidence for it. Sometimes people engage in "lazy referencing" based on the title or a very very quick look. Like in the previous case, this poor practice will catch up with you eventually.
  • ___ Make sure all your references are up-to-date, i.e. don't cite a paper as "submitted" when it is in press or published, don't cite an ACP Discussions paper when the final ACP version is available, etc.
  • ___ In the author-date format, references should be cited chronologically, not alphabetically. I.e. it should be "(B et al 2010; A et al., 2014)" and not "(A et al., 2014; B et al., 2010)"
  • ___ If a reference is used as part of the text, parentheses should be adjusted accordingly, e.g. "as discussed by Martinez et al. (2014), we follow..."
  • ___ If a journal uses numbered references (e.g ES&T), our internal review should still use author-date format, as that is much easier to read and thus makes the review process faster.
• Symbols, Formulae, and Units
  • ___ All mathematical symbols should be in italics, both in equations and in the text.
  • ___ All chemical formulas and mathematical symbols need to be subscripted or superscripted properly
  • ___ All Greek letters should be in "Symbol" font. No "um" for microns or "us" for microseconds and so on.
  • ___ Write units in the denominator as "-unit", not as "/unit." I.e. write g cm-3 and not g/cm3 and so on.
  • ___ Only m/z (in italics) should be used for MS mass/charge units. m/Q and the Th units are not understood by most folks and are confusing, and you should avoid them while in the group.
  • ___ Use lowercase italic d for particle diameters
  • ___ Use OA for organic aerosols, not "org" or others
  • ___ Only SI units should be used, unless an exception is essential.
  • ___ Avoid the term "loading" which has led to confusion in previous reviews, use "concentration" instead
  • ___ The symbol "#" for number doesn't translate internationally, use "No." instead
• Scatter Plots, Regression, and Correlation
  • ___ Remember that regression and correlation are different things, and come from different unrelated mathematical operations. A "correlation line" makes no sense, only a "regression line" does
  • ___ "Correlation plot" should not be used, use "scatter plot" only
  • ___ All regressions should be ODR (/ODR=2 in Igor) and this should be stated either in the methods section or in the relevant figure captions
  • ___ Whether an intercept is fit or fixed at 0 is a scientific decision based on what is known about the data being fit, sometimes it is appropriate to show both results
  • ___ Be careful with the use of qualitative expressions such as "good correlation", try to be quantitative when possible instead e.g. "R2 = 0.95"
• Figures:
  • ___ Introduce figures in the text as soon as you start describing the relevant results. It is confusing if a lot of results are discussed before the relevant figure is introduced
  • ___ Make the graphs of a sufficient size / aspect ratio / grouping so that they can be seen clearly in the review format (e.g. PDF as submitted, or ACPD / AMTD landscape pages) and in final publication.
  • ___ The meaning of all traces and symbols should be in the graphical legend, NOT in the main text or the figure caption.
  • ___ The figure captions should explain what the figures show (i.e. the evaporation rate vs time for systems 1 & 2), but not the scientific conclusions made from the figures. Those should be in the main text.
  • ___ All fonts in graphs (axis labels, tick labels, legends etc.) need to be of sufficient size to be readable in printed form or on the web. This means 10 pt font when pasting the graphs at their actual size (or equivalent size if changing their size after pasting into Word). This is the absolute minimum size, but larger is typically better if possible.
  • ___ As a practical rule to test the item above: put a 10 pt text box with the word "Test" next to each figure, if any text is smaller than that, make it larger (including graph legends, tickmark labels etc.). Do not send any papers to Jose until you have done this, as he is very tired of repeating this over and over.
  • ___ Use color if useful, but print all your graphs in B&W and make sure they are readable in that format too, if at all possible, by wise use of symbols, dashing, and shades. (For e.g. reviewers or readers who print in B&W, plus color-blind folks).
  • ___ All graphs should have this macro executed so that we can find them in the future. But for publication or presentation purposes this info should be hidden behind a white box.
  • ___ All figures (and tables) should be numbered in the ordered they are introduced in the manuscript
  • ___ All axes should start at 0 unless there is a strong reason to do otherwise, and have a zero line
  • ___ Dates should be in the format "6-Jan-2014" or similar, not as "1/6/2014", which would be interpreted as 1-June in much of the world
• Supp. Info
  • ___ The Supp. info will almost always be published as a PDF that we provide, thus make sure the formatting is clear
  • ___ Supp Info should start with "Supplementary Information for" (in 1 line) and then give the title and author list of the paper

What is the internal review process of a paper?

• Generally we will iterate through multiple drafts, with Jose, Doug, and other group members and coauthors reviewing the paper, followed by the first author generating a new version
• We will refer to the following levels of review:
  • Level 1: "big picture" review, looking at the figures, key sections, abstract, conclusions, with input of the scientific story of the paper and its quality, gaps etc. This is a notch up from reviewing an outline, but there is not detailed text reviewing other than maybe the abstract or critical areas.
  • Level 2: intermediate-level review, with detailed comments and some editing of the text, but where the first author will address the gaps thoroughly, followed by re-review
  • Level 3: thorough review, with the assumption that the paper can be submitted immediately after this review and its comments are addressed. (In practice there is typically at least one re-read).

What is the procedure for a quick "difference review"?

• Sometimes it is of interest to generate a "difference version" between two versions of a paper. E.g.:
  • Between the version that was submitted to a journal, and the revised version before resubmission
  • Between the version that was shared with coauthors, and the version that has been modified reflecting their input
• To do this, take the original version and accept all changes, and save it. Then do the same with the revised version. Then in Word go to Review --> Compare Documents, and select the original and revised document. Execute, and save the result. All the differences between the 2 papers should be marked as "tracked changes", which makes it easy to review the changes only.
  • If changes are extensive the "track changes" generated in this way may be so many as to be less useful, but it is always worth a try and it takes 2 minutes to try.

What is the procedure for sharing a paper draft with coauthors?

• The paper needs to be sent to all coauthors with enough time for them to review it, which is typically 2 weeks. The following text can be used as a starting draft for your email:

Dear Coauthors
Please find attached our paper entitled "XXX" that we have prepared for submission to journal "YYY". Please read the paper and return any comments or edits to us by XX-XX-20YY (2 weeks from the day you send the email), or let us know if you need additional time. At a minimum please review the spelling of your name, your affiliation, as well as any details describing and using data from your instrument / model etc., though comments in all parts of the paper are very appreciated. If you have multiple comments, using "track changes" in Word is best. Let us know if you have any questions at this time.
Regards,
-First author

• Then set yourself a reminder in Google Calendar to send a reminder email 1 week and 3 days from the due date (or some alternative of your liking). These reminders are very useful since our coauthors are typically very busy, and the reminders help to get the paper to the top of their queue.
• For people who have not replied to the first several emails after several days past the deadline, you need to send a last email before submission stating something like "The journal requires that we confirm that the submission has been done with the consent of all coauthors, so at the very least please confirm that you wish to remain a coauthor, or alternatively that you prefer to be moved to the acknowledgements section. If we do not hear from you after this reminder, we will move your name to the acknowledgements."
  • The names of coauthors who don't confirm that they want to stay indeed need to be removed from the paper before submission.

How do I submit a paper?

• The first author always submits the paper him/herself.
• You need to go to the online system of the journal in question, and upload the manuscript and Supp Info as PDF. Sometimes you also need to upload other documents such as copyright agreements, figures in specific formats etc. Refer to the instructions for authors of the journal you intend to submit to.
• For journals that have a length limit, some (e.g. GRL, PNAS) will not even allow you to submit if the paper is determined to be too long by an automatic checker. Others may allow you to submit (e.g. ES&T) but the paper will be rejected a couple of days later by the staff before it reaches an Editor. Thus it is very important to pay attention to the length limits.
• For several journals a letter to the editor is required. This should not be a repeat of the abstract. Rather you have to summarize:
  • What is the broad topic and the key finding(s) of the paper
  • Why is this paper appropriate to the journal you are submitting to. For this point it is good to refer to other papers on the same topic published in that journal, or to how many of the references you cite are in the journal you are submitting to.
  • Run this letter by Jose or Doug before submission.
• For journals that allow a "second contact" (including ACP and AMT), please enter Jose with his @colorado email address.
• We should discuss suggested reviewers. We typically try to suggest 10 reviewers so that the Editors have some options to choose from (though most Editors will choose reviewers not in our list as well).

What do I do after submitting a paper?

• As soon as the paper is submitted, you should send an email to all coauthors with something like:

Dear Coauthors
Please find attached the PDF of the submitted version of our paper entitled "XXX" that I just submitted to journal "YYY", for your records. We have done our best to address everyone's comments. If you have further comments, find any remaining mistakes etc., please let us know and we will address those comments together with the ones from the reviewers
Regards,
-First author

What are the group specifications for responding 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 is a bad idea 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 (those should NOT be highlighted).
• (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.
  • If the reviewer is asking multiple questions on a paragraph, respond to the most important one first. Alternatively, it is ok to break up the reviewer paragraph into subparagraphs (R1.1a, R1.1b...) and insert your response below each one.
  • All changes to the document text need to be given in quotes and in bold in this document.
  • Make sure to subscript, italicize, and otherwise follow all the group and journal format specs in the responses as you did for the paper. This communicates attention to detail to the Editor and Reviewers, and can help get the paper accepted.

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. For papers from our group, following this format is mandatory.
• 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:
  • This response document of Marr et al., ACPD 2006.
  • 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?"

If the paper goes to further rounds of review in ACPD or AMTD

• In these journals the reviews and responses to the first round of reviews are public, but later rounds are not. Changing this procedure to make later rounds public has been discussed at the Editors meetings of these journals, but for the time being things will stay as is.
• However the Editorial Board encourages authors or editors to add a final comment to the paper, posting the reviews and responses to further rounds of review, after EVERYONE involved (authors, editor, and referees) have agreed to such public posting. An example of a final comment along these lines is in the public discussion of this paper.

What are the group specifications for providing corrections for the proofs of a paper?

• For final papers (and for ACPD and AMTD also for discussion papers) the journals ask us to review a set of "proofs." Typically there are a few mistakes left and the journals introduce a number of errors while "copy-editing" the paper for publication. Typically we request 20-40 corrections for a particular set of proofs. Also figures are often small and sometimes of poor quality. Note that once the paper has been published, corrections can NO longer be made. Please adhere to the following specifications for this process:

___The first author will read the proofs completely, and check all the figures, tables, captions, references, and acknowledgements.
___Prepare a list of corrections in a new tab in this document in that format. (Or alternatively as corrections in the PDF file)
___Print the proofs to verify that they print correctly and the colors / figures etc. are readable.
___Read especially carefully the abstract and conclusions.
___Check the author list, including spelling mistakes and middle initials, as well as the affiliations.
___Check that Jose is listed as the corresponding author with the colorado email address.
___Check that the section numbers are correct.
___Check all the figures for quality, both in screen and in print.
___Check the size of all the figures, often journals make them too small in the proofs and they can be hard to read.
___Check the reference list for correctness. Update any papers that are in "discussions", submitted, or in press, if possible. Contact the authors of such papers if needed.
___Check that the acknowledgements thank the sources of funding that supported the work, if in doubt check with Jose.
___Either Doug or Jose will also read the proofs. The first author will combine them with his/her comments and send to the journal.
___Check the revised proofs in detail, and if completely correct approve for publication.
___If needed, the first author will iterate with the journal until the paper is approved for final publication. Note that journals typically introduce 1-2 new errors for every 10 errors they fix, but sometimes in can be much worse.

Can I be the corresponding author of a paper?

• Per tradition in the field, papers from the group have the supervisor as corresponding author. Since we collaborate with many groups, including some at CU, this is important to signal the paper as being primarily the product of our group. We rarely get emails via the corresponding author mechanism, and if we do Jose will forward them immediately.

Can I be a coauthor of someone else's paper?

• Authorship in our group is based on specific contributions to the work on that paper.
• The number 1 coauthor issue is that someone is left out by mistake. This happens A LOT, especially on papers using data from a lot of people etc. Don't assume that you've been left out on purpose before you ask.
  • Importantly, if you think you have been left out by mistake, you need to ask quickly, as it becomes difficult and eventually impossible to add authors as the paper progresses towards publication.
• If you have been left out of a particular paper (NOT by mistake) and you want to discuss it, please prepare a list of specific contributions to the actual material on that particular paper. If you convince us that there are enough specific contributions, then we can reconsider the decision (for papers from our group) or ask the main authors (for papers from other groups).
• There is not such a thing as "author trading", i.e. if someone is a coauthor in your paper, you can't be a coauthor in theirs just because of that
• For secondary contributions to a field or lab study, e.g. a person helped run an AMS but did not analyze the data nor do other analyses for the paper, the policy is that person will be included as a coauthor on the 1st paper (sometimes the first couple, depending on details) using the data, but not on latter ones.
• Note that for papers not from our group we do not have control over coauthorship decisions. We can argue for someone to be included, but the main authors may say no.
• Coauthorship issues do lead to a lot of tense discussions and stress at times. There will be times when one feels one has been left out of a paper one should have been a coauthor of. However in the big picture sometimes you may be included on papers that you contributed a small amount of work to, so it can average out in the big picture, and it is not worth getting really upset or making lifelong enemies based on this!

Why can't you review my paper faster? It is important for my fellowship / graduation / job application / etc.

• We try to work through draft papers as fast as we can, but producing high quality papers takes a lot of time, and there are many tasks that compete for that time. Any plans you make around publications have to take into account that our feedback may need many rounds, and each round will take some time, more so during busy times such as field studies etc. Also, at times Jose and/or Doug may be too busy for weeks (months on occasion) at a time and may not be able to read a paper immediately, although we will always try to do it ASAP. This happens in all research groups. You need to take this into account in planning timelines for paper submission, graduation etc. and build up enough buffer time to meet your personal deadlines.

Presentation FAQs

What are the group specifications for BOTH oral presentations and posters?

___ Go over the specifications for papers above and implement any that are applicable
___ File names should always follow the group file naming convention above
___ Include one of the new CU logos on the top left. (Available here)
___ Include the logos of all the relevant funding agencies (including for Fellowships) (Available here)
___ Make sure that you list as coauthors (or in the acknowledgements, if they prefer) anyone who has contributed substantially to the scientific process, or whose data you have used.
___ For preliminary data from others, make sure to ask for permission to show them in the presentation or poster
___ Only m/z (in italics) should be used for MS mass/charge units. m/Q and the Th units are not understood by most folks and are confusing, and you should avoid them while in the group.
___ All axes should start at 0 unless there is a strong reason to do otherwise, and have a zero line
___ All graphs should have this macro executed so that we can find them in the future. But for presentation purposes they should be hidden behind a white box.
___ Dates should be in the format "6-Jan-2014" or similar, not as "1/6/2014", which would be interpreted as 1-June in much of the world

What are the group specifications for oral presentations?

___ The most important aspect of a presentation is that the length works well to the time allotted. Make sure you know the time allowed (including introduction by the session chair, questions, and transition to the next speaker). E.g. in AGU talks are typically 15 min, but you only have 13 "net" minutes. Typically the material that you can present corresponds to 0.7-0.9 slides per "net" minute (depending on slide complexity, animations etc.).
___ All presentations should have a small but visible slide number in the TOP RIGHT corner. This can be added from the "Slide Master" view in powerpoint. This allows much faster feedback when preparing the presentation, and also more precise questions at the end of talks.
___ For presentation slides. All fonts in graphs axes, legends, labels etc. should be large enough that they can be read from the back of the room. Same for text in PPT slides. It is easy to underestimate this requirement, the equivalent of Font 18 pt (when typing directly into PPT) is needed. This rule is the one that's violated most often, please do not waste the group's time with axis labels, legends etc. that are difficult to read or unreadable.
___ As a practical rule to test the item above: put a 18 pt text box with the word "Test" on all slides (easiest if you put it on the Slide Master), if any text is smaller than that, make it larger (including graph legends, tickmark labels etc.). Do not show any presentations to Jose until you have done this, as he is very tired of repeating this over and over. This is the absolute minimum size, but larger is typically better if possible.
___ When presenting, remember that the audience tends to get lost in the big picture issues, while the presenter is often focused on 2nd and 3rd-order details. Remember to provide enough "framing" information, and to remind people throughout the talk about what you are talking about.
___ Think about the background that your audience has on your topic. It is your responsibility to keep connecting from where your audience is to where you are talking.
___ For group rehearsals, you need to be able to go through the presentation and tell your story in approximately the right time. Do not waste the group's time by showing up unprepared.
___ Before the conference, rehearsing multiple time to yourself (and sometimes with other group members) helps a lot to deliver a smooth presentation.
___ See these resources with more presentation tips

What are the group specifications for posters?

___ Check the conference instructions about the poster size. AGU is 6 ft wide x 4 ft tall, other conferences typically want narrower (4 ft wide) posters, but this varies a lot. Generally we want to go with the largest poster allowed, noting that the CIRES printer can only print up to 3.5 ft (42 in) wide (as of Dec 2014).
___ Please include one of the new CU logos on the top left.
___ Add a "Take Home Points / Conclusions" box at a prominent location in the poster (e.g. top center)
___ Make sure that the figures print at sufficient resolution.
___ For group rehearsals, you need to be able to go through the poster and tell 2 versions of your story: the 1-minute version, and the 10-minute version.
___ Send a copy to Jose or Doug for a final proofread before printing.

Computing FAQs

Does the group provide a laptop of desktop computer?

• Typically people start in the group with their own laptop. Once that laptop is too old or slow for group work, we typically buy one from research funds. Funding agencies have strict rules about when a laptop is allowed on a grant, and CIRES enforces these rules fiercely, so we can't always buy additional laptops, especially on short notice. If you will need a new computer, please let Jose know at least 3-6 months in advance.
• If you are using a group laptop, you will have to return it to us when you leave. If you are still working on papers or other group work, we may agree to let you keep the computer for some months until that work is complete. If we do this, it is your responsibility to pack it safely and ship it back to the group.

Is there an easy to use set of bookmarks for some of the frequently used group web pages?

• Yes. The following is a link to an html file that can be imported into Firefox (and possibly other browsers): J-Group.Bookmarks.html
  • If you left-click on the link, you will see a web page that has the links.
  • f you right-click on the link, select "save link as..." and save the file to your computer you can then import the bookmark:
    • If you are using Chrome: "Cntrl-Shift-o (to open bookmark manager) => Organize => Import bookmarks from HTML file..." option.
    • If you use Firefox: "Cntrl-Shift-b (to show all bookmarks) => Import and Backup => Import Bookmarks from HTML..."
    • If you use Microsoft Internet Explorer: click on the star icon (favorites) => Add to Favorites => Import and Export => Import from a file => Next => check favorites => Browse to the file you downloaded => Next => Select "Favorites Bar" => press "Import."

Can I use a Mac or Linux computer?

• Much of the hardware and some of the software we use is Windows-specific (e.g. Labview, Visual Basic, NIST MS database...), so a Mac or Linux-PC would NOT work. There are also many subtle incompatibilities when trying to share files between a Mac and a PC that can create a lot of delay when working jointly on papers or presentations. Macs or Linux computers do not work with some hardware we have encountered in the field (e.g. we found that Macs could not connect to certain network hubs or printers, and those were the only units available at the field site). Also, it is critical that people are intimately familiar with Windows so that they can diagnose and fix quickly problems that may arise with instrument computers or data acquisition laptops in the field or other experiments. Thus we use exclusively Windows PC computers (Windows 7 as of Dec. 2013).

Should I have a smartphone, and if so is there a preference on brand / carrier?

• Yes, as smartphones are critical tools these days for fast web searches, email, chats etc., which can be critical during field studies or at conferences.
• As of Jan. 2014 we recommend Android smartphones (with a larger screen), as many of us have those and they are more compatible with the many Google Apps that we use for group work. However some people have smartphones from other operating systems.
• As of Jan. 2014 we recommend Verizon wireless, as many of us have our phones there, and calls between Verizon subscribers are free, which can save a lot of money in field studies. However this is not enforced and there may be reasons to choose other carriers.

Will the group provide a tablet?

• No. As of Jan. 2014 we haven't found those to be critical to our work, since we all already have laptops and smartphones. Some people in the group have tablets that they purchased with their personal funds.

Am I expected to do regular backups?

• YES!! As of Jan 2012, everyone in the group is required to use two systems:
  • An automated backup via the internet using Carbonite. This is a paid service (covered by the group), and you should check with Phil for setting it up on your computer (we will be transitioning to an in-house solution as Carbonite licenses expire PLH 10/2014).
  • A local copy in a portable hard drive. You have to be disciplined about making a copy of your data and documents at least every week (better if every day), updating what you have changed during the week. We have seen a surprisingly large number of people loose work, sometimes months or even years of work, for not having an up-to-date backup. This is lessened if you have Carbonite, but Carbonite does fail sometimes and it is slow for getting all your data back. For this you should use the Viceversa Pro software for which we have a group license, and you should have your own portable hard drive from Apricorn.
  • Losing research data or other information due to lack of compliance with these guidelines is a serious offense.

Which software do we use?

In the group we use a pretty standardized set of software packages to do the different things we do. This is not to say that these packages are the best, I am sure we could do the same work with a completely different set of programs. However standardizing is very useful to be able to help each other learn and use the software and work effectively. You are REQUIRED to use the following packages in your work (any exceptions must be authorized by Jose):

• Standard Install - Computer/Software install and configuration.

• There are other programs which can do the same function (e.g. Latex instead of Word, OpenOffice, Matlab...), however there is a great benefit on using the same set of programs as we can learn from each other and share files easily. Therefore for group work you are expected to use the standard programs above.

• There is no standard email or web browser for the group, you can use whichever you prefer. GMail is quite useful, but some group members use Thunderbird or Outlook.

Can I use Matlab / IDL / R / etc. instead of Igor?

• No, for many reasons:
  • There is a big benefit to the group from using a standard data analysis software tool, as everyone can answer questions about how to do something or share pieces of code to do specific tasks. We also employ two Igor professional programmers who can always help with more complex problems. And code written by one group member is often re-used or adapted by other group members, and code written in e.g. Matlab or IDL would be useless to the rest of the group.
  • Our group uses instruments such as the ToF-AMS, Q-AMS, ACSM, ToF-CIMS, TSI SMPS, or data analysis techniques such as PMF or ME-2, for which extensive analysis software is available in Igor and only in Igor. This can't be changed any more than one could not viably translate entire climate models away for Fortran.
  • Anything that can be done with other programs can be done with Igor too. At the end, the arguments about 'the best' programming language are similar to e.g. those about 'the best car.' For most of us a car that we know how to use and can take us where we need to go safely and not consume our time is what we need. In my 11 years at CU, I have never seen a student or postdoc be limited by Igor as a language. People are limited by errors in logic, poor organization of their code, sloppy naming of variables and functions, lack of comments, etc. The data analysis programming of people in our program has always been limited by their own time, insight etc., but if it could possibly be done and it mattered to us, we have done it in Igor. I do know one former researcher who insisted in translating a lot of our software into Matlab because according to him "it was a superior language"... except he never got anything practical done despite a lot of effort and ended up leaving the field.
  • Igor is the dominant language in the field of Atmospheric Chemistry in which we work. Both the CU groups and most of the groups where our students go on to work as postdocs or researchers use Igor as a main tool. In field studies we often exchange data directly as Igor experiments or Igor binary waves. And knowing Igor well is a major advantage for postdoc or research positions that you may apply to when moving on from our group.
• Importantly, if you already know another programming language and you work on learning Igor, you will be up and running pretty quickly.
• The only exception would be if we had to use a software package that's already programmed in a different language and that would be too difficult to translate.

Conferences and Travel

What are the group rules for attending conferences?

• Attending conferences with all expenses paid by research funds is a privilege, not an automatic right, just for being in the group.
• A typical attendance level is 1-2 conferences per person per year.
• A new group member can attend up to 2 conferences, given that s/he has sufficient results at the time of abstract submission, before submitting his/her 1st first-author paper in the group. After each first-author paper published, each group member can attend up to 2 additional conferences, again if new results (not those in the published paper) are ready at the time of abstract submission.
• By submitting an abstract to a conference, you are committing to have a full draft of your presentation or poster ready by 2 weeks before the presentation. This allows sufficient time for the group to review the presentation and provide feedback. Violation of this rule can have consequences in reduced conference attendance in the future.
• Most of the group tends to go to (one or several of): the AAAR Annual Conference, the AGU Fall Meeting in San Francisco, the AMS Users Meeting.
• Other conferences such as the Annual Conference of the ASMS, ACS National Meetings, the Gordon Conference on Atmospheric Chemistry, the Annual Meeting of the EGU in the Spring (Vienna typically), etc., are possible if there are suitable sessions.
• Jose will send emails ahead of the deadlines for major conferences, and at the start of the year. You are responsible to maintain your preferences updated in the "Group Schedule" Spreadsheet under the "Conferences" Tab.
• Higher levels of productivity (>1 paper per year) or special needs (e.g. special sessions where the group needs to be represented) may lead to people attending more than 1-2 conferences per year.
• Lower productivity (e.g. no paper submission over the last year) may lead to not attending any conference that year. The fact that this rule is often not applied doesn't preclude that it may be in the future.
• In general the results to be presented need to be fully cooked by the abstract deadline. Exceptions to this rule are on a case-by-case basis.
• External funds (conference grants, certain fellowships) may allow additional conference attendance. Note however that funding agencies (e.g. NSF, NASA, EPA) often explicitly consider fellowships as an extension of the funding that they provide to the group, and they reduce our grants accordingly.
• Local conferences (in Boulder or Denver) generally don't count in this regard as the expenses are much smaller (transportation is free with RTD, and the group only covers registration). Note that grant rules prohibit travel reimbursements (such as per diem) if the conference is less than 50 miles from Boulder (e.g. Denver & Fort Collins) as it is considered "commuting."
• Conferences in other continents (e.g. Europe, Asia, Australia) tend to be far more expensive. Many grants cannot be used for foreign travel, and others have a lot of extra red tape. Therefore attendance of conferences abroad is less frequent, although possible.
• Final decisions combine all of these factors and will be made by Jose.

What behavior is expected at conferences and field studies?

• When you attend a conference, it is a professional trip where you are representing our group, and professional behavior is expected. Many other attendees will eventually judge the publication of our research (as referees and editors) and future funding for our group (as proposal reviewers or program managers).
• If others see you skip the conference to go sightseeing etc., or party late at night and get drunk, or don't get up in time for the morning sessions, our colleagues will notice and this could have a serious negative impact the group's future funding and research opportunities... and even more so on yours! Such behavior will not be tolerated and will certainly impact your attendance to future conferences.
• In particular we have had some problems with excessive alcohol consumption, going to sleep too late, or poor eating habits in past group-supported trips. These are often disruptive to other group members, especially if apartments, rooms or cars are being shared or if joint work is needed. We will be watching this closely in the future.

Do we need to share rooms while on travel for field studies or conferences?

• Yes, as funding agencies do not provide sufficient travel funds for all productive group members to attend conferences. If we did not share rooms, we would need to cut the amount of travel by a lot, including many fewer people going to conferences.
• For field studies, sometimes a single room is available (e.g. due to an odd number of people present). In those cases the people staying the longest in the field study have priority.

What are the rules for per diem (meals) travel reimbursement for the group?

• The total reimbursement is limited by the US government per diem rate for that location. If you spend more, it is on you (this is a CU rule, not the group's).
• The group policy is that you should request reimbursement of the actual meal expenses, beyond what you would have spent in meals if you had stayed at home, not the full per diem. This is done because the per diem rates are often very high, and cannot be supported with the travel funds provided by the funding agencies, especially for long field studies. By claiming the actual increase in meal expenses, we save travel funds to have sufficient people in the field, and for group members to attend conferences. Receipts are not needed.
• If a group member decides to go to expensive restaurants or drink a lot or drink a lot of beer, those are personal costs and not something a grant should cover, so requesting extra per-diem for those reasons is not valid.
• Often we will set a common per-diem rate for a given field campaign or conference. Typically $20 or $25 / day as of Jan. 2015.
• Note that if the conference / meeting is less than 50 miles from your regular place of work (e.g. conferences in Denver), Federal Grant rules do not allow any reimbursement of travel or per diem. I.e. it is considered commuting, and you couldn't be reimbursed either for driving to your regular workplace or meals there.

Do I need a driver license?

• Yes, since our group participates in many field studies where driving is required.

Are there any special requirements for renting a truck to move equipment?

• Yes. Any truck with a GVWR (Gross Vehicle Weight Rating) of 10,000lbs or more used for official business requires specialized training for the University's compliance with DOT regulations, and to ensure that you are insured.
• In general any truck over about 12' will have a GVWR of 10,000lbs or greater.
• Please see the Practical_Ref Wiki for more deailed information.

Group Service FAQs

If I join the group, am I supposed to do anything else than research?

• YES.
• Graduate students may work as a teaching assistant (TA) during some semesters.
• Everyone in the group is expected to perform at least one significant service task per year, e.g. maintaining some instruments etc. This helps us all by making the group run smoothly and ensuring that our infrastructure (e.g. instruments) is working. Most of the time this will be very low intensity (few hrs/week), although there will be some periods in which more work will be required.

How is Group Service organized?

• Tasks are assigned in Asana/Grp Mgmt for each instrument, piece of software etc.
• A summary of the tasks is also kept in http://tinyurl.com/jg-plan
• People should enter a comment with the frequency requested in the task noting that everything is working, or any problems and action plan, or that the item is not in use etc.
• These assignments are updated once a year as part of the performance review process. They can also be updated more frequently if needed, per agreement of all the parties involved.

What are the Standards for Lab Safety, Cleanliness, and Organization?

• By joining the group, you are accepting to maintain high standards of safety, cleanliness, and organization in the lab. We don't care if some other's group lab is less clean or organized, that's their problem. We need to all work on this on a day-to-day basis. E.g. we should not have scattered items on the various counters. Please put things (tools, pens, tapes, cables...) away IMMEDIATELY after you use them. Everything should have a place in the drawers / cabinets. If it does not, choose an empty drawer or cabinet, put the stuff in, and label it appropriately (the labeling materials are in the "office supplies" drawers towards the front of the lab), and ALSO enter the change in the Group Organization "Lab Inventory" Spreadsheet

• Be especially careful NOT to lay any cables or tubes on the ground or at a low height, as these are accidents waiting to happen. Route all cables and tubing high off the ground.

• If there is a cable tray in the vicinity, all cables and sampling lines should be located in there. All cables and lines should be NO LOWER than the cable tray height. NOTHING should be below cable tray height unless it is really really really the only way to do it. We may disassemble lines and cables that do not comply with this policy and ask you to redo them.

• If you are working on a given location and want to keep some tools nearby, get a transparent plastic bin, label it as yours, and keep everything there.

• If we let someone else use our lab (don't do this unless you check with Jose first), make sure that they understand the rules for safety and organization in our lab. Please make sure that they take their stuff (and leave ours) after they are done.

• For cardboard packing boxes, there are only two possible fates:
  • If we decide to keep it (which we should do for expensive stuff that we may return for repair, such as instrumentation), write on them what they are for (e.g. "DMA Column") in big letters, and store them safely on the shelves or on top of the cabinets. If they are very large, check with Michael to bring them to storage in East Campus.
  • If we are not keeping the box, recycle it that same day, when you leave for the evening. The corner near the entrance of the lab is NOT a storage location for boxes. Each group member is responsible for this for the items s/he orders & uses.

• Recyclables (paper at least) in the lab are not picked up very often. If you see the recycling person, please ask him/her to come to the lab that same day, and to continue coming on a regular basis.

• If anyone (from our group or other groups) borrows a tool or something else from us, please ask them to sign it out on one of the sign-out sheets near either lab door. This is extremely important. Of course do the same if you borrow something from e.g. Maggie's lab. If they don't have a sign-out sheet, put a post-it on their door.

• Please remember that we have lots of rechargeable batteries. The chargers (one universal, the other Ni-Cd only) are by one of the windows to the atrium. Please be careful not to throw away rechargeable batteries as these are expensive. Also if in the field, or if loaning stuff to people in other labs, please let them know about the rechargeable batteries. You'd be surprised how many of these get thrown away by people who do not pay attention.

• Food may be stored in the student office refrigerator or inside a closed plastic tub in your desk. We had mice a few years ago, and we need to avoid that in the future. Please no food of any kind anywhere else. Also don't leave food wrappers etc. in the trash in the lab, as they can also attract mice. The microwave in the lab is for drying silica gel and other lab uses, not for food.

What are group member's responsibilities for monitoring the literature?

• Each group member is responsible for monitoring certain journals, and posting and commenting on interesting article on the Google+ literature community
  • See above for people + journal

Vacation FAQs

How much vacation do we have in the group?

• The current policy (which is set by CU) is two weeks (10 working days) a year of vacation for graduate students. See below for extra vacation after intense field studies.
• Postdocs and research scientists have a separate system in which they accrue vacation days with time. The CIRES human resources people can explain the details of this system.
• Please put the days you'll be away in the Group Google Calendar.
• Please let Jose know of your intent to take vacation if the vacation is longer than 3 days, or if it happens less than 6 weeks before a field study or conference that you are attending.

Can I take off for Spring Break or Fall Break?

• No, unless you choose to take some of your regular vacation during that time. Note that the Spring or Fall Breaks are only breaks from classes, and it is NOT a vacation period from research. In fact we often work on research more intensely during those periods as people have more time since classes are not held that week.

Can I take vacation BEFORE field studies and conferences?

• Please do not schedule vacations within a month of an important deadline (two months if possible). Breaking this rule without discussing with Jose first will be penalized. Examples include an upcoming field study, a conference you may be presenting at (AAAR in October and AGU in December are the main ones), a paper deadline, etc. Experience shows that these periods are very intense and your continuous presence is needed.

Can I take vacation AFTER field studies or conferences?

• Field studies can be very draining, with continuous 12-hr workdays for several weeks and no weekends. Obviously one needs to recover after these, and the periods right after field studies are good to take time off.
• For the same reason, scheduling your vacations AFTER a deadline (conference, etc.) is generally a very good idea.
• In recognition of the intensity of some of our field studies, group members which participate in a field study may be able to take extra vacation, corresponding to the number of weekend days that they worked during the study. E.g. if the study was 4 weeks long, including 4 weekends, and there were only 2 off days, then the group member can take an extra 8 - 2 = 6 vacation days. These days should preferably be taken soon after the field study. Some less intense field studies do not qualify for the full policy, and in all cases this should be discussed with Jose first, and the final arrangement must be recorded via email to Jose.

Specific For Graduate Students

When can I graduate with a PhD?

• A Ph.D. thesis is composed of at least three high-quality peer-reviewed journal papers. The condition to schedule a PhD thesis defense is that at least 2 papers must be published, and a 3rd must be submitted to the journal (after dealing with any issues and with agreement of all the coauthors).
• If you are interested on a career in research, it may be highly beneficial to your future career to take advantage of the typically high productivity at the end of a PhD to write additional papers. However this will not forcibly delay your graduation.
• We will support your applications for postdoctoral fellowships and positions once you are within a 6 months or so of graduation, which typically means that two of your papers are published, and we are iterating on the edits of a full draft of the 3rd paper. Applying for postdocs (or other jobs) earlier than that tends to be distracting and not really useful since you don't know when you will be available to take a position, and that timing is typically very important for employers. The graduation rule will not be change if e.g. you were to apply for a postdoc on your own and obtain a position, and then fail to graduate in time according to the above rule, due to e.g. complications in data analysis and writing of your last paper.

When can I graduate with a Masters?

• For a masters based on research, the criterion for graduation is to submit at least one high-quality paper to a peer-reviewed journal.

What is a typical schedule for progress during a PhD?

The schedule below would be typical, although it can vary due to the needs of individual projects, impact of field projects, being lucky with early results, and especially working hard!

• Year 1: take 4+ classes, TA both semesters, pass cumes (CHEM), join research group, start working on research.
• Year 2: take rest of classes, take written comps in Jan. (ATOC), work intensely on research, pass oral exam, initial draft of 1st paper by end of 2nd year (Aug).
• Year 3: take oral comps. by Dec. (ATOC), complete draft of 1st paper by Dec, submit by Apr, published by Aug. Initial draft of 2nd paper by Aug.
• Year 4: complete draft of 2nd paper by Jan, submit by Apr., publish by Aug. Initial draft of 3rd paper by Aug.
• Year 5: complete draft of 3rd paper by Jan, submit by May. Defend thesis in June, finish corrections and graduate in July.
  • Note 1: The years above are all academic years starting in Sep and ending in Aug.
  • Note 2: An initial draft is a complete outline with all figures in draft form using actual data. A complete draft has all text and complete references, in addition to polished figures.

How is the summer percentage of salary determined?

• This summer percentage is calculated with a mathematical formula from your performance rating of the last 2 reviews.
• As a research group our "products" are new knowledge, crystallized in publications, and training of researchers. If research is not published in a timely manner, it may as well not have been done. Therefore submission or publication of 1st author journal paper during the last year will result on a higher salary during the next summer. This rule only applies to the summer of year 3 or later in the PhD process.
• Starting for the review of calendar year 2014, students on their 3rd year or later who have not submitted or published any 1st author papers over the last 2 calendar years can only receive at most a rating of "Meet Expectations" and summer salary pay of at most 60% FTE. To be clear about the dates, a student who started in Fall 2012 would be in their 3rd year during the group review process of calendar year 2014, which will take place in Spring 2015.

• The funding situation of the group can also influence summer salary levels from year to year, but higher performing students will continue to be compensated better than lower performing ones with the above method.

Specific for Research Staff & Postdocs

How are salary raises allocated?

• Each year CU determines the salary pool percentage. Our group total raise cannot exceed that pool. Depending on the funding situation we may or may not be able to match the pool amounts, though most years we do match it.
• After the performance review process (using our improved version of the CIRES ASA) during the Spring, salary raises are calculated with a mathematical formula, proportional to the performance rating. The salaries are typically effective Oct. 1st of the same year.
• As a research group our "products" are new knowledge, crystallized in publications, and training of researchers. If research is not published in a timely manner, it may as well not have been done. Therefore publication of 1st author journal papers during the last calendar year will result on a higher salary raise. (This rule does not apply to group members whose primary task is not research).
• Starting for the review of calendar year 2014 (that will take place in Spring 2015), postdocs & research scientists who have been in the group for over a year but have not submitted or published any 1st author papers from their group research in the last 2 calendar years can only receive at most a rating of "Meet Expectations".

When can I apply for faculty or research positions after the group?

• You need to have published (or at least submitted) at least one journal paper (2+ being much better) from the research that you have conducted in the group to have the full support of the group for such applications. If your publication output is non-existent at the time of application, in general I will not send a letter. Even if I do send it due to special circumstances, the letter will be perceived as weak since I could only talk about your great publications... that are "in preparation." As a prominent Caltech scientist told me once: "if a paper is in preparation, it doesn't exist. Papers only start having some value for the external world when they are submitted."

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