Forum: What Do You Waste Your Time On
13
gravatar for Asaf
3.8 years ago by
Asaf4.0k
Israel
Asaf4.0k wrote:

Like in everything else we do, the 80%-20% rule works great in bioinformatics. What is your 80% of the time wasted on? I can suggest:

  1. converting accession numbers between databases
  2. parsing output
scripting forum bioinformatics • 6.4k views
ADD COMMENTlink modified 4 months ago by i.sudbery990 • written 3.8 years ago by Asaf4.0k
42
gravatar for Michael Dondrup
3.8 years ago by
Bergen, Norway
Michael Dondrup40k wrote:

www.biostars.org ;)

ADD COMMENTlink written 3.8 years ago by Michael Dondrup40k
24
gravatar for zx8754
3.8 years ago by
zx87543.6k
London
zx87543.6k wrote:
  1. Converting one file format to another file format.

  2. Converting one file format to another file format.

  3. Converting one file format to another file format.

ADD COMMENTlink written 3.8 years ago by zx87543.6k
21
gravatar for Emily_Ensembl
3.8 years ago by
Emily_Ensembl10k
EMBL-EBI
Emily_Ensembl10k wrote:

Asking people to clarify their question.

Pointing people towards the free online help/tutorial/documentation that already answers their question.

ADD COMMENTlink written 3.8 years ago by Emily_Ensembl10k
2

"Asking people to clarify their question" This has to be number one for me.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Eric Normandeau9.2k
1

After some more thoughts, the process is more akin to helping them to formulate their own questions...

ADD REPLYlink written 3.7 years ago by Eric Normandeau9.2k
2

I spend 80% of my time actually reading documentation. But I'm one of a very small number of people who actually do that I think...

ADD REPLYlink written 3.8 years ago by Mary11k
2

What do you mean? Could you please clarify?

ADD REPLYlink written 3.7 years ago by polarise360
13
gravatar for Medhat
3.8 years ago by
Medhat6.1k
Poland
Medhat6.1k wrote:

learning how to :) over and over

ADD COMMENTlink written 3.8 years ago by Medhat6.1k
2

sadly!...=)

ADD REPLYlink written 21 months ago by dago2.0k
11
gravatar for Zev.Kronenberg
3.8 years ago by
United States
Zev.Kronenberg10k wrote:

Arguing with my lab mates about variant calling pipelines.

ADD COMMENTlink written 3.8 years ago by Zev.Kronenberg10k
2

so what is the verdict?

ADD REPLYlink written 3.7 years ago by Matt Miossec320
2

The point is there isn't one :-). Depends on the project.

ADD REPLYlink written 3.7 years ago by Zev.Kronenberg10k
11
gravatar for Woa
3.8 years ago by
Woa2.5k
United States
Woa2.5k wrote:
  • Trying to find more new tutorials on subjects that I already know much about

  • Browsing references citing one article, and references citing them and references citing them .....add infinitum

  • Downloading lot of journal articles thinking that their algorithms will come handy some day

  • Browsing through random codes, by goggling filetype:python etc.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Woa2.5k
10
gravatar for Jeremy Leipzig
3.8 years ago by
Philadelphia, PA
Jeremy Leipzig16k wrote:

replacing files, versioning, pruning, waiting for stuff to finish running

ADD COMMENTlink written 3.8 years ago by Jeremy Leipzig16k
3

yeah, the waiting thing kills sometimes

ADD REPLYlink written 3.8 years ago by Pavel Senin1.8k

I always try to race the program.  If I can write a faster version before it finishes running, or add substantial-enough improvements to make the output of the original obsolete, I kill it and start over.  That puts a bound on how slow my programs can be - they never take longer to run than they do to write :)

ADD REPLYlink written 19 months ago by Brian Bushnell9.8k
8
gravatar for Ashutosh Pandey
3.8 years ago by
Philadelphia
Ashutosh Pandey10k wrote:

Comparing results from different methods takes a lot of time too.

ADD COMMENTlink written 3.8 years ago by Ashutosh Pandey10k
8
gravatar for biorepine
3.8 years ago by
biorepine1.2k
Spain
biorepine1.2k wrote:

Installing packages and relevant version of perl and python X.X.X.X.... with out admin privileges :)

ADD COMMENTlink written 3.8 years ago by biorepine1.2k
1

Oh, yeah, this is what kills me the most, Our cluster is not connected to internet for security reasons and image for for R or perl when you are installing a package that has a lot of dependencies. Also if one package works only with recent R versions, make me sick :)

ADD REPLYlink written 3.7 years ago by Sirus710
2

https://github.com/pengchy/RScript/blob/master/download_r_packages.R

may be this script will help you. 

this script is used to 1) download the latest source packages to local; 2) update local source packages; 3) download dependencies of one specified package

ADD REPLYlink written 21 months ago by pengchy310
6
gravatar for Rm
3.8 years ago by
Rm7.4k
Danville, PA
Rm7.4k wrote:

book keeping, debugging, keeping pace with version changes of the tools

ADD COMMENTlink written 3.8 years ago by Rm7.4k
7

For version 2 we decided to change every flag, just to make things more interesting.

ADD REPLYlink written 3.8 years ago by Zev.Kronenberg10k
6
gravatar for venkateshr89
3.7 years ago by
venkateshr89640
United States
venkateshr89640 wrote:

Trouble shooting for several hours when I Install packages which cannot run just because of outdated python or R version (that too without having system admin privilege)

ADD COMMENTlink written 3.7 years ago by venkateshr89640
6
gravatar for dago
21 months ago by
dago2.0k
Germany
dago2.0k wrote:

Forgetting to use the -w flag in grep, and therefore repeat all the analysis!!!


ADD COMMENTlink modified 21 months ago • written 21 months ago by dago2.0k
4
gravatar for Giovanni M Dall'Olio
3.8 years ago by
London, UK
Giovanni M Dall'Olio24k wrote:

The following is an example of R code. It contains a small error, which when hidden in a >200lines scripts causes an error message that is incomprehensible to most human beings. Can you find it?

myarray = c(1,2,3,4,5,)

Most of my time goes wasted fixing silly R syntax errors like this. I really wish Python had more libraries for working with large datasets and plotting :-/.

ADD COMMENTlink written 3.8 years ago by Giovanni M Dall'Olio24k
2

Have you looked into rpy or rpy2?

ADD REPLYlink written 3.8 years ago by KCC3.7k
5

http://pandas.pydata.org worth a look

ADD REPLYlink written 3.8 years ago by Jeremy Leipzig16k
1

Thank you for both answers :-) But for now I have all my code in R, maybe next time I'll try with pandas.

ADD REPLYlink written 3.8 years ago by Giovanni M Dall'Olio24k
2

Simple, the last comma.

ADD REPLYlink written 3.8 years ago by Raygozak1.1k
1

Are you kidding? Try using R to operate on terabyte hdf5 files.... Have you seen matplotlib? mayavi? Who would waste their time debugging R when you can use better tools in Python? You can always wrap your old R code using Rpy.

ADD REPLYlink written 3.8 years ago by schryer10
4

You shouldn't be trying to read huge files with R, but you also probably shouldn't be trying to do complex statistics in python. The right tool for the right job. :-)

ADD REPLYlink written 3.7 years ago by Chris Miller17k
2

Actually I find that R has a wider range of options for reading large files than python. You have the rhdf5 library from bioconductor, the sqldf library that allows you to read csv files to a database instead of keeping them in memory, and much more. I have used with great results PyTables for reading HDF5 in python, but I just find that R has more options.

ADD REPLYlink written 3.7 years ago by Giovanni M Dall'Olio24k
1

useful information, when I met large data, I will first try shell, then perl. I will try the rhdf5 library in the future.

ADD REPLYlink written 21 months ago by pengchy310
1

If R error messages were more informative, it would already be a huge improvement. What about simply telling us on what file/line the problem is happening?

ADD REPLYlink written 3.7 years ago by Eric Normandeau9.2k
4
gravatar for pengchy
21 months ago by
pengchy310
China
pengchy310 wrote:

Rerun the analysis after finding a bug in the scripts, or found a wrong parameter used, or new data input. 

ADD COMMENTlink written 21 months ago by pengchy310
3
gravatar for Noolean
3.8 years ago by
Noolean2.9k
State College, PA, USA
Noolean2.9k wrote:

Searching for data and their quality check.

Searching for hours and hours just to find out that such data does not exist yet. Or that although in 1000 HGP does exist excel with families, they have not been sequenced yet. Trying to find out if the reads are genomic/RNASeq, who published them, male/female and so on..

Converting between formats.

Installing new software.

Waiting for results. I am no good in doing 5 things at the same time :-)

ADD COMMENTlink written 3.8 years ago by Noolean2.9k
3
gravatar for Pals
3.7 years ago by
Pals1.3k
Finland
Pals1.3k wrote:

Figuring out which tool to use. Lately, for analyzing miRNA data. Any pipeline suggestions?

ADD COMMENTlink written 3.7 years ago by Pals1.3k
3

I suggest you take a look at the questions with an miRNA tag on the forum: mirna. You can "Limit to:" recent answers (top left) and "Sort by:" answers or votes (top right) to help you find useful info.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Eric Normandeau9.2k
3
gravatar for Anima Mundi
19 months ago by
Anima Mundi2.1k
Italy
Anima Mundi2.1k wrote:

Reinventing the wheel ;)

ADD COMMENTlink written 19 months ago by Anima Mundi2.1k

I do that all the time.  Totally worthwhile!  It's as least as useful as exercising on a treadmill, but more fun.

ADD REPLYlink written 19 months ago by Brian Bushnell9.8k

True, while most time the use of existing tools would save me time and even provide me better solutions, reinventing the wheel is definitely fun and instructive!

ADD REPLYlink written 19 months ago by Anima Mundi2.1k
2
gravatar for Nari
3.8 years ago by
Nari800
United States
Nari800 wrote:

In here, answering others' questions. :)

ADD COMMENTlink written 3.8 years ago by Nari800
2
gravatar for enunvillafer
3.8 years ago by
enunvillafer100
Cuba
enunvillafer100 wrote:

functional interpretation of protein lists from comparative proteomics studies

ADD COMMENTlink written 3.8 years ago by enunvillafer100
2
gravatar for Raygozak
3.8 years ago by
Raygozak1.1k
State College, PA, Penn State
Raygozak1.1k wrote:

Meddling with incorrectly annotated genes/proteins.

ADD COMMENTlink written 3.8 years ago by Raygozak1.1k
2
gravatar for forum42008
19 months ago by
forum4200820
Cebu City, Philippines
forum4200820 wrote:

A waste of time comes with a loud indicator: Just see how you feel after an activity. Are you energized or drained by it? Are you happy or resentful for it? You know the feeling when you’ve wasted your time. I find all of these a giant waste of my time, but if you don’t, well that’s why we have the comment section, so tell me what you think.

ADD COMMENTlink written 19 months ago by forum4200820
2
gravatar for alolex
19 months ago by
alolex810
United States
alolex810 wrote:

1) Trying to stay organized.

2) Debugging my scripts because a new dataset broke them in an unanticipated way--and just when I thought they were robust to all errors :(

ADD COMMENTlink written 19 months ago by alolex810
1
gravatar for i.sudbery
4 months ago by
i.sudbery990
Sheffield, UK
i.sudbery990 wrote:
  • Making sure all the analyses I rushed off in an excited whirl are properly written up and documented in reports/notebooks where I should have done them in the first place. Making sure all the labels are rotated correctly, the titles in plain english, the color viewable to color blind people etc....

  • Managing branches across a codebase with 15 collaborators across three forks and tens of branches.

ADD COMMENTlink written 4 months ago by i.sudbery990
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