Draw chart easily with Draw.io

Hi all,

We all need once in a while to draw a big flow chart or something else with blocks and arrows. I was looking for a nice and free solution and came across https://www.draw.io/

It works as an browser app that can be integrated with Google Drive (thus benefitting from the cloud storage). It is simple to use and help to create nice things very easily.

Thought it was worth sharing 🙂

If you know other good tools of this kind, please share in the comments!

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Job manager for power

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We all get asked and keep asking each other “how do you manage your power jobs?”. So here’s one possible answer. I have a few general-purpose functions that help me (1) generate jobs; (2) submit & prioritize (which jobs must run before others); and (3) monitor their run & investigate errors in a consistent manner across projects. If you wish to see what they’re like, you’ll find some documentation & code, and an online example linked here.

OmicTools for finding software

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I recently found OmicTools, an index of available packages / software / web interfaces / databases for analyzing various types of -omics data (RNA-seq, Ribo-seq, methylation, Hi-C, etc.). As you may know, almost any technology already has dozens of overlapping tools available for use, and this site helps to put order into this profusion. The only downside is that there are not many user comments / reviews at the moment so there is not much to guide your choice (aside from the original research papers, documentation, citations). Nevertheless, I recommend to check this site out, you might discover something useful.

Free WiFi at international universities

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Greetings from Cambridge. I have struggled in the past day with persisting unconnectivity around town and campuses. But then, Shlomit (tuller lab alumna) brought to my attention the eduroam network, which is available across the world in many universities. As TAU students, we can login using our TAU user/pass. Keep that in mind next time you’re abroad (or even in Israel), and see more info here and here.

 

Reference Management

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We all come to a point when we need to organise our references/citations. Obviously, if you have more than 3 references, you need some kind of manager to do it for you. For example, you want an automatic formatting based on the journal, and easy way to integrate the references into your document, a bibliography section generator etc.

Here you can find a great thorough comparison between many solutions, but for me it was kind of overwhelming, so I decided to narrow-down the options and parameters based on the lab’s experience.

Below the three most popular options, which are also used by different lab members. Note that Tamir (as of January 2018) is using EndNote. Also visit the following links for more in-depth comparison: [1], [2], [3], [4], [5], [6].

reference managers table

As a final tip, it is good to know that you can always get a citation file (e.g. in .ris format) from Google Scholar and import it to your software (in case the native option fails):

reference managers google scholar

Thanks to Alon, Michael and Hadas for useful information and links 🙂

 

Other free services for students

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@ofekschnitzer‘s amazing advice last week for unlimited cloud services made me realize that my @post.tau.ac.il mailbox does not contradict with the more recent @mail.tau.ac.il addresses that are issued to “new” students (feeling so old…). I could just login to Google using the latter, and even found a few emails waiting for me there!

The next thing to do, naturally, was to download the free student version of Office365 (which requires a @mail.tau.ac.il address). [Thanks, @oriahmio, for the advice!]

Recently I also signed up for GitHub Education, which provides premium GitHub services for developers, and is affiliated with many other services (Amazon Cloud, Microsoft Imagine, etc.). [Thanks, Michael and @doronka, for the advice!]

EDIT: JetBrains are giving all the professional versions of their precious IDEs (including PyCharm) for free to students with a university mail account.

I’m curious, what other student freebies do you know of?

 

Easy and free method to backup ALL of your data

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Hello everybody,

As you may have heard, Google education users get unlimited storage on their accounts, meaning that in our university Gmail accounts (name@mail.tau.ac.il) we have unlimited storage space. (I even found students online claiming that they uploaded a few Terabytes of data without any problem).

In order to use this unlimited storage efficiently, you can download Google’s Backup and Sync tool, which allows you to transform your google drive to a backup-storage folder. After you download the tool and link it to your university account, you will be able to choose folders from your computer that will be automatically backed up to your drive after each change/update in these folders.

It is working perfectly and smoothly for me, as the only issue was that the initial upload to the drive took few days due to the slow upload internet speed and the large amount of data.

 

Google’s Back up & sync download link:

https://support.google.com/drive/answer/2374987?hl=en&visit_id=1-636510797271432608-1072126729&rd=2bh

 

Ofek.

Themes for matlab’s IDE

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Happy new year, everyone! Many of us have recently upgraded our matlab version, and change is in the air. If, in addition (or instead), you feel like experimenting with a new look for your matlab IDE, consider trying Matlab Schemer. This package allows one to easily configure all the colors displayed within the IDE, e.g. for backgrounds, and syntax highlighting. A gallery of available themes can be found here. See if any of them catches your eye.

Color palette inspiration

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Doron’s great post earlier this week on fancy color gradients has left us with an open fundamental question – how to choose color combinations? While there’s no explicit answer to this, I was reminded of some awesome relevant online tools that, frankly, I should use more often. Since we’re all into figurework this week, here are a few picks, each with its distinct approach.

Perhaps the most intuitive source of inspiration is an image with a color composition that you really like. Palette Generator will build a palette from any such image that you upload.

Screen Shot 2017-12-28 at 0.08.09.png

COLOURlovers is a community-based site with countless palettes uploaded (and voted) by users, for those who choose to follow the aesthetics of the crowd.

Coolors is a color roulette. You never know what you’re gonna get. Just press the spacebar multiple times until you hit something you like, then adjust it a bit to your taste.

Adobe has an interactive palette picker, where every action affects all colors in your palette, until tuning is complete. You may also use it to employ a few color theory rules of thumb.

Hadas once sent me a link to a matlab function that returns RGB values for “intuitive” color names in natural language (based on a thorough xkcd survey of the spectrum). Envious Python users should check out seaborn.

Finally, most of the above sources provide HTML colors (in hex format, such as #06D7FF). Nevertheless, they can be easily converted to matlab RGB colors, for example using a function such as:

function cmap = hex2rgb(varargin)
n = length(varargin);
cmap = zeros(n, 3);
for i = 1:n
 assert(ischar(varargin{i}) && (varargin{i}(1) == '#') && (length(varargin{i}) == 7) && all(ismember(varargin{i}(2:end), '0123456789aAbBcCdDeEfF')), 'expecting hex/html color format: #RRGGBB')
 cmap(i, 1) = hex2dec(varargin{i}(2:3))/255;
 cmap(i, 2) = hex2dec(varargin{i}(4:5))/255;
 cmap(i, 3) = hex2dec(varargin{i}(6:7))/255;
end

Here it is at work, to set discrete colors for your plots:

>> colormap(hex2rgb('#773300', '#bb5533', '#eeaa99'))

And as basis for fancy gradients:

>> colormap(colormapCreator(num2cell(hex2rgb('#773300', '#bb5533', '#eeaa99'), 2), [0.5, 0.5], 10))