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
• 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). As of July 2012 these are:
  • Lab AMS: Doug
  • HIAPER AMS: Pedro
  • "MAB/TAG" HR-AMS: Pedro
  • MOVI-CIMS: Reddy
  • DMAs and CPCs: Pedro
  • Filter sampler: Patrick
  • OPC + DusTrak: Brett
  • Valve switching system: Brett
  • Thermal denuder: Patrick
  • PAM and associated analyzers: Brett

• 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.

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

In general the answer is YES, but pls write it on the clipboard which is attached to the door of the lab BEFORE the item leaves the lab. 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.
• 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 10 am to 4 pm, so that interactions with other group members are possible.
• 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.
• 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).

Publication FAQs

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.

Why can't you review my paper faster?

• 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 time Jose and/or Doug may be too busy for weeks 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.

Computing FAQs

Can I use a Mac or Linux computer?

Much of the hardware and some of the software we use is Windows-specific, so a Mac or Linux-PC would NOT work. There are also many subtle incompatibilities when trying to share files betwen a Mac and a PC that can create a lot of delay when working jointly on papers or presentations. Finally Macs 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). Thus we use exclusively Windows PC computers (mostly Windows 7 as of Jul. 2012).

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 Michael for setting it up in your computer.
  • 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.

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):

• CU antivirus
• Igor Pro (data analysis and graphing)
• Skype (fast communication) -- you are required to be logged into Skype during working hours (including at least 10am to 4 pm every day, unless marked otherwise in the group calendar)
• Powerpoint (presentations)
• Excel (simple data analysis)
• Word (papers)
  • Microsoft Office is downloadable from here (CU campus license)
• Adobe Acrobat (PDF making)
• Viceversa Pro (local HD backups)
• Carbonite (online backups)
• This Wiki (web pages)
• CU VPN (accessing CU resources remotely)
• Google Docs (shared documents on web, some papers)
• Google Spreadsheets (shared spreadsheets, field study organization)
• Google Desktop (searching your own computer)
• Google Reader (keeping track of the literature with RSS feeds)
• WinSCP (secure FTP program)

• 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, but that has yet to happen in more than 10 years of group experience.

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).
• Conferences abroad (especially in Europe) tend to be much more expensive and many grants cannot be used for foreign travel. 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?

• 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 especially future funding for our group (as proposal reviewers or program managers). If they 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 in our future funding and opportunities. Such behavior will not be tolerated and will certainly impact your attendance to future conferences.

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, 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 expenses, we save travel funds for group members to attend conferences. Receipts are not needed.

Group Service FAQs

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

• YES. You may work as a teaching assistant during some semesters. Also you will be expected to do some service to the group every year, rotating in various roles. 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. Examples include instrument maintenance, organization of the AMS Clinic, and literature alerts.

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 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.

• 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 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 the third is in preparation. 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?

• There are two performance-based metrics that influence this.
  • 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 any 1st author papers 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.

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 (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."

Acknowledgement

By signing below, I certify that I have read the above policies and procedures and agree to abide by them.

Print Name:___________________________________

Signature: ___________________________________ Date: ______________

I have the following comments on these policies and procedures (write below):