Forum:What Do You Waste Your Time On
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8.0 years ago
Asaf 8.6k

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
bioinformatics scripting Forum • 11k views
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49
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8.0 years ago

www.biostars.org ;)

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28
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8.0 years ago
zx8754 10k
  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.
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24
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8.0 years ago

Asking people to clarify their question.

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

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3
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"Asking people to clarify their question" This has to be number one for me.

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1
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After some more thoughts, the process is more akin to helping them to formulate their own questions...

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2
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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...

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2
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What do you mean? Could you please clarify?

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16
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8.0 years ago
Medhat 8.9k

learning how to :) over and over

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2
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sadly!...=)

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13
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8.0 years ago
Woa ★ 2.8k
  • 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 .....ad infinitum
  • Downloading lot of journal articles thinking that their algorithms will come handy some day
  • Browsing through random codes, by goggling filetype:python etc.
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12
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8.0 years ago

Arguing with my lab mates about variant calling pipelines.

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2
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so what is the verdict?

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2
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The point is there isn't one :-). Depends on the project.

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10
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8.0 years ago

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

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3
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yeah, the waiting thing kills sometimes

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0
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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 :)

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8
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8.0 years ago

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

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8
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8.0 years ago
biorepine ★ 1.5k

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

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1
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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 :)

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2
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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

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0
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use conda package manager! ;) or linuxbrew..

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0
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Ah, conda is ok, just don't spam your base envir and you gotta be fine ;-)

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7
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6.0 years ago
dago ★ 2.7k

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


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6
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8.0 years ago
Rm 8.0k

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

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7
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For version 2 we decided to change every flag, just to make things more interesting.

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6
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7.9 years ago
venks ▴ 720

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)

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0
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use conda manager! ;)

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5
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8.0 years ago

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 :-/.

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2
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Have you looked into rpy or rpy2?

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1
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Thank you for both answers :-) But for now I have all my code in R, maybe next time I'll try with pandas.

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2
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Simple, the last comma.

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2
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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?

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1
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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.

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4
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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. :-)

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4
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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.

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1
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useful information, when I met large data, I will first try shell, then perl. I will try the rhdf5 library in the future.

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4
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6.0 years ago
pengchy ▴ 430

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

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4
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5.9 years ago
Anima Mundi ★ 2.8k

Reinventing the wheel ;)

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0
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I do that all the time.  Totally worthwhile!  It's as least as useful as exercising on a treadmill, but more fun.

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0
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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!

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3
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8.0 years ago

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 :-)

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3
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7.9 years ago
Pals ★ 1.3k

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

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3
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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.

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3
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5.9 years ago
forum42008 ▴ 30

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.

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3
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4.6 years ago
  • 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.

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1
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Aye to the rushed analyses and the last-minute documentation. Horrible, but somehow it happens all the time.

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2
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8.0 years ago
Nari ▴ 900

In here, answering others' questions. :)

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2
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8.0 years ago
enunvillafer ▴ 100

functional interpretation of protein lists from comparative proteomics studies

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2
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8.0 years ago
Raygozak ★ 1.4k

Meddling with incorrectly annotated genes/proteins.

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2
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5.9 years ago
alolex ▴ 910
  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 :(

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0
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5 weeks ago
cicindel ▴ 70

Figuring out how a dataset file had been created (i.e. "Is this the right file? How was it filtered?").

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0
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4 weeks ago
ponganta ▴ 220

Reinventing the wheel. Like, all the time. Why use clusterProfiler with an up-to-date GO-annotation, when you can just write your own client for PANTHER-ORA? Oh, PANTHER does not report genesets back. Why not just write a custom GO-slim for semantic extraction of cognate genes? I guess you only learn by making mistakes.

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0
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17 days ago
Juke34 ★ 5.7k
  • Trying to understand formats that have

    • too verbose documentation: it take years to understand the subtilities (exception, trap, etc...) or
    • too poor documentation: You end up by reading the code to understand the subtilites or you end up by doing try and fail method until you found how to use it for your purpose, until you have search again because you need it for another tool that need it in a different way.

=> The day you will be confident how to use it, the format will change (updated) or be deprecated, and you start over

  • Trying to understand tools that have

    • too verbose documentation: it take years to understand the subtilities (specific vocabulary and format, exception, trap, etc...) or
    • too poor documentation: You end up by reading the code to understand the subtilites or you end up by doing try and fail method until you found how to use it for your purpose, until you have search again because it does not fit for your new purpose

=> The day you will be confident how to use it, the tool will change (updated) or be deprecated, and you start over

In the past it was a lot about installing tools and dealing with dependencies to get previous tool still working, compilation, etc. Nowadays this task is a routine, but time to time we still find a tool that is a pain to install.

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