Currently Solicitating Content Suggestions for a LaTeX Seminar

LaTeX (pronounced Lay-Tek) is a powerful document preparation language developed by and for scientists for writing manuscripts, journal articles, and even presentations. I’ve blogged about various aspects before here and  here on Upsection.

My advisor and I are currently organizing an Intro to LaTeX seminar for grads and u-grads here at McGill. Content we’re planning on covering includes:

  • Getting started with LaTeX (selecting and installing TeX software) 
  • General journal formatting, templates, dictionaries, and style files 
  • Figures and captions 
  • Tables 
  • Equations and special characters 
  • Building your reference library 
  • Resources, help, and cheatsheets 
  • Adapting your manuscript to McGill’s LaTeX thesis template (something I’ll be doing soon and I’m sure other MSc and PhD students will be interested in).

Are there any topics we’re missing? The purpose of the seminar is not to be all-encompassing, but to provide enough direction and resources to get students started with using LaTeX.

So what helped you when you started using LaTeX? Any tips or advice we should share with our students? Let us know in the comments!

What do you do with reviewer comments?

A few months ago I submitted a grant proposal requesting money to perform some tests on a small aspect of one chapter of my PhD research. My grant proposal was rejected. I wasn’t surprised, this was the first grant I had ever written, so surely it was far from perfect. I could have expanded the importance of my research, gone into more detail on the analysis to be performed, worked harder on the accompanying figure, ect. When a grant proposal is returned (either accepted or rejected) to the author it includes feedback from the reviewers. In this case the reviews had a specified format for the reviewers to follow: i.e. Objectives and comments, Significance and comments, ect. I was quite surprised at the disparity between the two reviewers opinion’s of my proposal. 

For instance Reviewer #2 said the problem I was addressing was “Clearly Defined”, the significance of my project was “Interesting/Novel/Innovative” (the form probably just had check boxes for the reviewer to click), and that my methodology was “Clearly stated, well conceived and success likely”. Awesome, right?
Reviewer #1 disagreed. The problem I was addressing was “Not defined”,the significance was “Unacceptable”, My methodology was “Too vague to evaluate chances”. The accompanying comments from Reviewer #1 indicated that there was a complete disconnect and lack of basic understanding with my field of study, so far that I’m guessing the review wasn’t a geologist?). I will give them the benefit of the doubt in that my proposal was probably the billionth proposal they had read, that they had read it late at night long after the 10th cup of coffee had worn off, and that they were skimming every other sentence. Based on Reviewer #1’s comments it is clear that they did not know the terms, jargon, and ideas I was discussing. The proposal was supposed to be written for a general geology audience, so maybe I should have defined more terms. However, there was a tight word limit for each section of the proposal so I had to pick which jargon I should define. If I defined every piece of jargon I used that’s all my proposal would have been, with no discussion of what I actually wanted to do or how my idea is significant. Also, a quick Google search for one of the misunderstood terms yields a clear and simple explanation in the first result.
Based on Reviewer #2’s comments it is clear that they completely understood my proposed project and why I wanted to do it. Reviewer #1’s comments show they didn’t read my proposal. So where do I go from here? How do I find that middle ground where I demonstrate that I know what I’m talking about, still connect to a general audience, and stay within the word limit. I guess in future proposals I will have to set aside space to define terms.
What are your thoughts? As a reviewer do you have time to look up unfamiliar words or concepts? Do you have any stories of particularly useless reviews? Or particularly useful reviews for that matter?

#SciWrite update and day two of Geocon 2012

Alright this day started off with exciting news. My #SciWrite manuscript was accepted with moderate revisions.  This is the first manuscript I’ve ever written and was too excited to make the morning Geoconvention 2012 talks. Instead I spent time reading through reviewer comments and emailing with my co-authors. Can you blame me?

How I felt upon hearing the news my manuscript was accepted with moderate revisions.

In lieu of morning talk coverage, here’s an owl:

and an owl cleaning itself

Eventually I closed my laptop and popped into the Future Petroleum Resources of Canada III: Arctic Archipelago in time to see Dylan Tullius discussed the reservoir potential of the early Cretaceous Isachsen Formation in the Sverdrup Basin. He gave an excellent talk and had beautiful slides. I stuck around after the coffee break for Ashton Embry’s talk on episodic tectonism recorded in the depositional history of the Sverdrup Basin.

After lunch I sat in on the Carbonate Sedimentology session. The highlight of that session was a talk given by Graham Banks on porosity in northern Iraq carbonate reservoirs. Graham and his team found fine-grained carbonates with a complex fracture network that created a high permeability reservoir. They utilized a fracture analysis tool called the Sky Held Imaging Tool (whoever came up with that name didn’t think it through) to map fracture patterns with stitched images. Graham showed two very cool photos of bitumen seeping out of an outcrop wall. The session wrapped up with a talk by Stephen Longfield and Hadi Slayman on combining facies analysis and geostatistics to model reservoir permeability.

Yellow Bank Creek Complex #SciWrite DONE! and more news

So I finally finished my #SciWrite manuscript. I just submitted a manuscript to G-Cubed: Geochemistry, Geophysics, Geosystems. The manuscript was based on my undergraduate thesis at UC Santa Cruz on the Yellow Bank Creek Complex, the world’s largest known exposed sand injectite complex. It’s an amazing outcrop. I’ll be writing a field trip guide for the outcrop in the near future, a version of which will be posted here. I’m very excited to finally get it off my desk. Now I can get back to blogging! And onto planning summer field work, grading those labs…

Northern side of Yellow Bank Creek Complex outcrop. Yellow-tan sandstone is limonite cemented. Blue-grey sand is dolomite cemented.

Also, now that I have a submitted manuscript I updated my CV with it and finally set my McGill webpage live. I have a lot of awesome pictures posted there. Check it out. Please if you have any comments about that site (or this site too!) I’d love to hear feedback. Am I missing something crucial to my webpage that every grad student should have?, ect. Let me know!

I also want to work on a re-design for this blag, that’s on my farthest backburner, though. Any ideas?

Under Attack: What to do when your poster is under fire #AGU11

I by no means am offering solutions to this. Instead I hope readers in the comments will help out by posting their past experiences with this situation and detailing how they’ve handled it. That said, I need your help to make this post work! First, my poster experience.

My poster session at #AGU11 went really well. I was at my poster for the full four hours and never got a chance to leave. I was talking the whole time and getting great, positive feedback on my research, and some ideas of where to take it further. 
One gentleman did attack my work. The primary discrepancy came in the fact that he disagreed with outcrop features that I had interpreted as being cross-cutting. He had not personally been to the outcrop, but it was difficult to continue the discussion into the more interesting parts of my research because he would continually cut me off with “that’s not cross cutting.” Basic outcrop information that I had gotten across to everyone before (and after) was not getting to him. I must say it caught me off guard. This was my first time presenting a poster, and I was not sure how to handle this situation. I did my best to have a discussion with him, but it was very frustrating. 
Overall my first poster presentation was a positive experience, and it reignited my drive to finish my #SciWrite manuscript.
So please, readers and fellow GeoBloggers, if you (and/or research) has been attacked at a poster session please post the story and your insights in the comments section!

#SciWrite update

My posting rate has dropped dramatically in the past weeks. After AGU I headed down to Santa Cruz and couch surfed for a week before finally making my way to San Luis Obispo to be home for the holidays. I’ll hold myself back from talking about all the awesome Mexican food and beer I’ve been consuming…

Progress on my manuscript has been short coming. Gotta say it’s hard to keep working when it’s so nice out and a friend calls up to go hiking/drinking/riding/shooting/ect. Also, finally got a new laptop to replace my dying Dell machine. So now photoshop and illustrator are back online to work on figures.

In short, by the end of today I want to have my discussion section finished, and hopefully figures updated. Will go hiking up Bishop’s Peak as a break/tantime/exercise.

#Sciwrite update: Week 2

It’s been two weeks since Anne at Highly Allochthonous posed her writing challenge. Last week I posted a backwards calendar for what I need to get done before the AGU Fall meeting:

December 4th, 8am: Fly out to San Francisco for AGU.
December 3rd, 5pm: Department Christmas party. Definitely no work is getting done after this. Must be packed for AGU, and cook a dish for the party. Manuscript should be done and off my desk.
December 1st: Abstract done. Off my desk for revision.
November 25th: Poster deadline for AGU print services. Poster must be completed, reviewed, completed again. Includes all new data, figures, ect. This is the BIG ONE.
November 14th: Discussion will be written. After this I’m going into 100% poster mode to get my figures done.
November 12th: Results and Interpretation will be re-written to incorporate new data.

So how did I do?

I didn’t quite have my results and interpretation finished by the 12th. As for my discussion, got that finished last night.

Even though I’m making progress, I feel a little behind schedule because I’ve been putting of making the figures I need, pretty and publishable. This is a time consuming process, because I want my figures to be awesome.

How’d you do on your #Sciwrite goals?

SciWrite Writing challenge update: Week 1

Figure 1: twitter hashtag…

So a week has gone by since Anne at Highly Allochthonous issued a writing challenge to meet a deadline before the annual AGU conference in San Francisco. Many people have joined the challenge and have been tweeting updates of their accomplishments on twitter with the hashtag #Sciwrite. Anne  posted an update today, which reminded me that I needed to post mine!

In Anne’s update she also includes a “backwards calendar” listing the deadlines she needs to accomplish before AGU.  I’m going to set this up and share it to make myself more accountable.

How’s it going?
This week I’ve been working to collect more microstructure data. This consists of circling grains in images of thin sections. It’s dreary work, and very easy to brush aside with a “I’ll do that later.” To make myself get it done, I made a bet with my officemates. If I did not have all my data collected by November 7th I would spearhead getting us a coat rack or improve our office in some way (or beer). So far I’m the only one who has adopted this motivation method of negative consequences.

Anyway, I’ve been circling away in illustrator with an awesome tablet my adviser bought for our research group. It makes the circling go way faster than with a mouse.

Why circle grains? I’m processing them with an image analysis Matlab script that gives me tons of information including the area of the image that is grains, area that is matrix, grain orientation, aspect ratios, ect. I’m working with a lithic arenite, so the script needs a bit of help with picking out the grains. That’s where the dreary task of hand circling grains comes in.

Am I making process?
Short answer: Hell Yea!

Long answer: Now that my data has been refined, some statistical differences between images that previously went unnoticed are now apparent (sorry no details until AGU!). This is great news to us as it gives us something better to work with. Data to back up hypothesis? YES!

At AGU I’ll be presenting a poster. I plan on printing my poster using their in house poster service. The deadline for that is November 25th. So essentially I have two deadlines running. One for poster printing (very high priority) and one for manuscript (slightly less, but still very high priority).

So as for my backwards calendar, here goes:
December 4th, 8am: Fly out to San Francisco for AGU.
December 3rd, 5pm: Department Christmas party. Definitely no work is getting done after this. Must be packed for AGU, and cook a dish for the party. Manuscript should be done and off my desk.
December 1st: Abstract done. Off my desk for revision.
November 25th: Poster deadline for AGU print services. Poster must be completed, reviewed, completed again. Includes all new data, figures, ect. This is the BIG ONE.
November 14th: Discussion will be written. After this I’m going into 100% poster mode to get my figures done.
November 12th: Results and Interpretation will be re-written to incorporate new data.

This feels pretty tight as it is. Then I remember all the stuff I have to do for classes… busy end of the semester! Let’s GO!

Join #sciwrite and get that manuscript done.

Anne Jefferson over at Highly Allochthonous has organized a writing challenge. The idea is just to state your goals for manuscript writing either on your own blog or in the comments on the above link. Every Sunday you post a new update sharing what you’ve accomplished in the past week to move your manuscript/project forward.

Anne’s idea:

Here’s the plan. Use the comments below to tell me what you want to accomplish in the next 5 weeks. Each Sunday evening, I’ll stick up a post summarizing what I’ve accomplished during the past week, and what I need to get done in the next week order to reach my goal. You can do the same in the comments or on your own blog (with a link in the comments here, please!) During the week, we can use whatever means we please, such as reviving Brian Roman’s old #sciwrite tag on Twitter, to keep in touch, provide encoruagement, and brag about our progress. By December 4th, we will have reached our goals and we can go out for a virtual or real celebratory drink. Maybe I’ll even come up with some sort of prize or badge to reward participation.

My goal is to have my manuscript from my undergrad research at UC Santa Cruz ready to submit by the AGU Fall Meeting (Dec. 4th). I’ll be presenting a poster on the research there so I really need to get everything done before then.

This week I performed and reviewed grain analysis on thin sections to expand/solidify our data.

So head over to Highly Allochthonous and join the #SciWrite team!