Comments for What You're Doing Is Rather Desperate

Comment on How to: remember that you once knew how to parse KEGG by Kevin

Kevin — Wed, 15 May 2013 16:54:29 +0000

“Coincidentally, someone asked the same question at Biostar.” lol nothing truly happens by coincidence … I echo liam’s thoughts on rediscovery of things I once knew but hopefully with each rediscovery I am improving how I am doing it or learnt something new.

Comment on How to: remember that you once knew how to parse KEGG by liamthompson

liamthompson — Sun, 12 May 2013 15:24:28 +0000

Haha, “rediscovery of things I once knew” is a huge one for bioinformatics, I’m always rediscovering things.

Comment on The end of Google Reader: a scientist’s perspective by collectedrcode

collectedrcode — Fri, 19 Apr 2013 12:25:52 +0000

I don’t think RSS is dead because other people tell it’s dead. We have a diverse working environment in our lab. Sadly, only two out of 13 people use RSS feeds, I think. But for the two of us, it’s productive. One used the gO.ogleReader, and now has to switch. I simply use Thunderbird (portable) as RSS client; works fine and gives me what I need in most cases. My two cents: cloud stuff is pretty, but also quite fluffy and puffy. It can be blown away by the Higher Authority at any time. I’m going to stick with downloading my feeds (and mail, etc.). I can have a copy of stuff in a cloud service at the same time.

Comment on The end of Google Reader: a scientist’s perspective by Kay at Suicyte

Kay at Suicyte — Mon, 15 Apr 2013 14:05:59 +0000

I am currently trying ‘netvibes’ which also imports the google data and appears to work decently. The look & feel is somewhat unusual and requires some configuration work; I strongly prefer the reader mode over the widget mode, but this is a matter of taste. I also don’t like the fact that netvibes displays all feeds, no matter if there are unread items. However, after some time I got used to this feature and just ignore the feeds that are greyed out.

Comment on The end of Google Reader: a scientist’s perspective by nsaunders

nsaunders — Mon, 08 Apr 2013 21:17:15 +0000

I think you’re right regarding lack of genuine alternatives. I can’t see how Old reader, a toy side project run by 3 people, is going to scale to millions of users.

Comment on The end of Google Reader: a scientist’s perspective by Rohan

Rohan — Mon, 08 Apr 2013 15:02:08 +0000

The Old reader seems to be the most familiar and simplified online RSS aggregation, but sadly is quite buggy at the moment. Hope it clears up.
And Feedly seems to be reluctant to render LaTeX images, at least from wordpress.
As of now, there is no true alternative on the cloud (IMHO). Hope the announced digg Reader is up to the mark.

Comment on Git for bioinformaticians at the Bioinformatics FOAM meeting by nsaunders

nsaunders — Thu, 04 Apr 2013 23:49:07 +0000

I believe that Git can handle “quite large” files, but in general, I don’t believe in versioning data. I take the approach that if scripts operate on (unchanging) input files to generate output, then versions of output data can always be regenerated from versions of scripts.

I initialize git in the top level directory of a project and add sub-directories which don’t contain code (data, scratch etc.) to my .gitignore file.

Comment on Git for bioinformaticians at the Bioinformatics FOAM meeting by cotsapas

cotsapas — Thu, 04 Apr 2013 15:25:38 +0000

I should say that for now I’m initializing git within src/ to track code only…

Comment on Git for bioinformaticians at the Bioinformatics FOAM meeting by cotsapas

cotsapas — Thu, 04 Apr 2013 15:24:53 +0000

So, you’ve finally convinced me to stop just editing scripts :) I’m using git on locally only, with one repository per project. I still haven’t figured out if I need a “remote” repository (e.g. another local dir) to push to. I don’t think so, unless it’s a cross-project codebase sort of thing.

What’s your feeling about large datasets in git? My project directories usually have src/ bin/ data/ analyses/ log/ dirs within them, with (sometimes large) data living in data/ .

Comment on The end of Google Reader: a scientist’s perspective by glennstrycker1981

glennstrycker1981 — Thu, 04 Apr 2013 14:38:22 +0000

A friend of mine suggested that we all use Google+ exclusively, as many feeds are available as people to follow on G+. This option does not work for arXiv.org RSS feeds, which are very important for scientists to read. I just switched over to theoldreader.com, and it seems to be a much nicer interface for reading paper abstracts than feedly. Theoldreader has the same look and feel as Google Reader. Still, I miss having all of my data in one place on the cloud (Google).