September 2011
2 posts
30 tags
pomodoro technique
Umesh recently discussed the Pomodoro Technique (slides), a time management method that uses a timer to break down tasks into 25-minute intervals called ‘pomodori’ (PDF book on PT, book on PT). The work intervals are separated by brief breaks, usually five minutes each. The name comes from the tomato-shaped kitchen timer that was used by Francesco Cirillo, the inventor of the method,...
26 tags
scientific publishing
Niko Kriegeskorte from the MRC Cognition and Brain Sciences Unit at Cambridge recently discussed the future of scientific publishing (his blog on this). He considered these questions: What’s good and bad about the current system? What features define the future system and how can we transition to it?
Good things about the current system include that it provides a signal of what to read. It...
August 2011
5 posts
23 tags
version control
Rich recently discussed version control (slides, notes for Git with Ubuntu and NYU). Version control, which is also called revision control or source control, is ‘the management of changes to documents, programs and other information stored as computer files’. Rich started with some ideas on what you might use it for and why you should use it. One use is for synchronization. You have...
6 tags
speaking
Greg Steinbruner of Applied Speaking and Presenting recently discussed public speaking, in his words speaking to a purpose. He started by reminding us of some things. Liking speaking, or not liking speaking, does not correlate with how good you are at speaking. Speaking is a performing art. When you speak, you are simultaneously in a vulnerable and a powerful position.
Greg described a tripart...
30 tags
preparing manuscripts
I recently discussed the preparation of manuscripts. My focus was on how you can increase the efficiency and accuracy of the process of collective writing. My thoughts are derived from, and geared towards, the kinds of writing that we do in LCV. I include some thoughts on using LaTeX and BibTeX, for example, which are widely used here, but may be relatively uncommon, or unheard-of, elsewhere....
13 tags
14 tags
blogging
Jeanne Garbarino recently discussed her observations about the science blogosphere (her Prezi about it, her post about it).
Her first point was that there is science communication directed to scientists, which takes the form of journal articles (e.g., PLoS ONE), conferences (e.g., Cosyne), grants (e.g., NRSA Individual Postdoctoral Fellowships) or other stuff within a research institution (e.g.,...
July 2011
5 posts
16 tags
adding publications to your cv
Umesh recently discussed how to automate the ‘Publications’ section of LaTeX-based CVs (associated files, example CV). His desiderata for Publications: reverse chronological order; organization by type (e.g., for journals, conferences, abstracts and talks); and his name in bold. He doesn’t want to enter this stuff manually and he’d like it to match what shows up on his...
11 tags
adding publications to your website
Rob recently discussed how to add your publications to your website using his bib2php, which, as the name implies, converts BibTeX to PHP. bib2php was developed at LCV for this purpose, to add all of the lab’s publications to the lab’s website. Here is what the output looks like. I’ll describe some of this more below, but note that the main output shows lists of publications, with the standard...
20 tags
sleeping
Pascal recently discussed sleep, the first part in a series on how to build a successful and sustainable life in science (or maybe even a life in life). He first covered cultural attitudes towards sleep. The attitudes he’s observed are: sleep is for losers; at best, it’s a waste of time; great people don’t sleep very much; no sleep equals success; the real elites get by on little...
30 tags
making figures
Umesh recently discussed making figures with Inkscape (video tutorials), whose motto is ‘Draw Freely’, which we’ll get to (associated files). Inkscape is another vector graphics editor. It’s free and open source (information about open source alternatives). You can use it to edit figures generated using MATLAB and can also use it to make posters for conferences.
Umesh...
11 tags
making figures
Deep recently discussed making figures with Intaglio. Here is a summary of his thoughts on it in terms of pros and cons. It is fast and light weight (i.e., not a resource hog). It’s relatively cheap. We looked into pricing and believe that it costs $89 compared to $199 for the student version of Adobe Illustrator or $599 for the commercial version. It could be said that your lab or...
June 2011
4 posts
13 tags
making figures
Jeremy recently discussed making figures with Adobe Illustrator (associated files). I’m going to summarize the points he made starting with some of his thoughts on writing, design and choice of software. Writing can be thought of in terms of tone, organization, conceptual clarity, concision and precision, all objective qualities. While style can be debated, consistent style gives you a...
18 tags
exporting figures
Rich recently discussed creating and exporting figures from MATLAB (associated files). He started by listing the things he wants: to produce a figure for a paper (e.g., for LaTeX); for fonts, line widths, etc. within the figure to be a specified size (e.g., 12 pts); for fonts and symbols in the figure to be identical in the text; to automate the process as much as possible since regenerating the...
30 tags
managing references
Jess and Alick from Mendeley recently visited us at NYU, with Jess leading a discussion on using Mendeley for reference management (slides). She covered these features: (1) adding content; (2) managing content; (3) sharing content; and (4) discovering content. I should say that, considering an analysis of reference management tools that we thought of yesterday, we’re likely to call these...
7 tags
May 2011
7 posts
30 tags
sharing code and data
I recently discussed an aspect of open research that is of particular relevance to our lab, which is releasing the code and data associated with a project (slides). The general topics of open research and open science are already quite broad, and are evolving. Sharing everything, the end of publishing as we know it (as reason for not worrying about being scooped), alternative means of review, were...
4 tags
17 tags
managing references
Umesh recently discussed reference management using Zotero (slides). One should hardly need to be convinced that it’s better to use any reference management tool than to print everything you read. It might be like considering whether it’s better to write emails or handwritten letters for everyday communication. In one case, there is no search, no ordering and no easy way for grouping,...
10 tags
18 tags
writing faster code
Rob recently discussed writing faster MATLAB code (i.e., code that takes less time to run) (slides). Answers to “why should I care,” include that you don’t want to wait for results and your labmates don’t want to wait for your results. I think that faster code also allows you to do more. For example, faster code might allow you to search a larger portion of a space, or...
8 tags
13 tags
unit testing
Rich recently discussed unit testing, an important aspect of his coding practice (slides; sample code). So what is unit testing and why is it important? The idea of unit testing is to write a collection of tests in parallel to writing code. The tests are on units, defined as the smallest piece of testable code, and they confirm that the units are fit for use.
You can probably convince yourself...
April 2011
2 posts
6 tags
18 tags
inception
Four of us from the Laboratory of Computational Vision (LCV) at NYU are starting a small meeting to discuss essential tools for scientists. Our focus is largely technical and the list of topics we plan to discuss includes many about programming, software, and computing. Besides technical stuff, we intend cover other topics that we consider to be important to our lives as scientists, such as time...