Question: Distributing And Tracking Work Among Bioinformaticians
8
gravatar for Ryan D
6.8 years ago by
Ryan D3.3k
USA
Ryan D3.3k wrote:

We have a project that has several components that we want to distribute across a network of bioinformaticians. For instance:

  1. Identify common variants from 1kG
  2. Identify structural variants from TCAG
  3. etc.

And there are about 25 items on the list. Rather than forwarding emails where each person says they volunteer for #1, #7, #14, is there a website or tool that would allow people to select tasks and update their progress on those tasks? A kind of tool that might allow one to select the tasks that they are doing and possibly indicate that they are X% done or enter a note about what remains to be completed.

Any suggestions (or tag edits) are appreciated.

Rx

workflow • 2.5k views
ADD COMMENTlink modified 6.7 years ago by Gustavo520 • written 6.8 years ago by Ryan D3.3k

similar question: http://biostar.stackexchange.com/questions/58/what-is-the-best-way-to-share-scripts-between-members-of-a-lab

ADD REPLYlink written 6.8 years ago by Giovanni M Dall'Olio26k
8
gravatar for Pablo Marin-Garcia
6.8 years ago by
Spain
Pablo Marin-Garcia1.8k wrote:

Jira, redmine etc.. is the way you go when you want fully detailed history an control of the project but has a lot of overhead (like having a server and maintaining the installation....) when you only want you only want something for people to volunteering for tasks and have a log of the % of completion. For this, the simpler thing is a spreadsheet in google as someone else suggested, but if you want to have a bit more of info an control, web pages as trello (still free and created by Joel Spolsky* ) or PivotalTracker (now need subscription) are very good, simple and intuitive.

* Joel Spolsky is one of the creators of StackExchange (The framework used by BioStar). You can see his blog entry for trello here

ADD COMMENTlink written 6.8 years ago by Pablo Marin-Garcia1.8k
1

Thanks Jira and Sean. Both Redmine and Trello look extremely useful. Trello, in particular, looks really cool with instant synchronization between browsers. Redmine has nice displays which allow progress and number of hours to be tracked. For our next project, I think we'll try one of these (probably Trello) out.

ADD REPLYlink written 6.8 years ago by Ryan D3.3k

Thanks Jira and Sean. Both Redmine and Trello look extremely useful. Trello, in particular, looks really cool with instant synchronization between browsers. Redmine has nice displays which allow progress and number of hours to be tracked. For our next project, I think we'll try this out.

ADD REPLYlink written 6.8 years ago by Ryan D3.3k
4
gravatar for Istvan Albert
6.8 years ago by
Istvan Albert ♦♦ 78k
University Park, USA
Istvan Albert ♦♦ 78k wrote:

I would try generic project management tools like Basecamp.

The problems that you need to solve a that of information transfer and coordinating between people; non-bioinformatics oriented tools ought to work well.

ADD COMMENTlink written 6.8 years ago by Istvan Albert ♦♦ 78k
3
gravatar for Gjain
6.8 years ago by
Gjain5.2k
Göttingen, Germany
Gjain5.2k wrote:

Hi Ryan,

The most common ones:

There are many subtools available that helps these kinds of collaboration very easy and makes it more manageable.

ADD COMMENTlink written 6.8 years ago by Gjain5.2k

I think Google Docs seems easiest to use. People can edit the spreadsheets and documents and we see the updates instantly.

ADD REPLYlink written 6.8 years ago by Ryan D3.3k

In our lab and my previous company, we use google docs extensively.

ADD REPLYlink written 6.8 years ago by Gjain5.2k
2
gravatar for Sean Davis
6.8 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

I have been using redmine for this type of thing. Redmine is a flexible project management web application. Written using the Ruby on Rails framework, it is cross-platform and cross-database. Redmine is open source and released under the terms of the GNU General Public License v2 (GPL). Setup is quite straightforward and quick.

Some of the main features of Redmine are:

  • Multiple projects support
  • Flexible role based access control
  • Flexible issue tracking system
  • Gantt chart and calendar
  • News, documents & files management
  • Feeds & email notifications
  • Per project wiki
  • Per project forums
  • Time tracking
  • Custom fields for issues, time-entries, projects and users
  • SCM integration (SVN, CVS, Git, Mercurial, Bazaar and Darcs)
  • Issue creation via email
  • Multiple LDAP authentication support
  • User self-registration support
  • Multilanguage support
  • Multiple databases support
ADD COMMENTlink written 6.8 years ago by Sean Davis25k
1
gravatar for Niallhaslam
6.8 years ago by
Niallhaslam2.2k
Dublin
Niallhaslam2.2k wrote:

The openatrium tool was mentioned on here before and looks good but might be a little overkill. I'd go for the google docs suggestion as in the setup costs are nil.

ADD COMMENTlink written 6.8 years ago by Niallhaslam2.2k
1
gravatar for Gareth Palidwor
6.8 years ago by
Gareth Palidwor1.6k
Ottawa
Gareth Palidwor1.6k wrote:

I would recommend BaseCamp in conjunction with shared data and source directories as well as source control.

The data pipeline should be defined in advance to ensure that everyone isn't running off in different directions making slightly different assumptions

ADD COMMENTlink written 6.8 years ago by Gareth Palidwor1.6k
2

There are many project collaboration sharing systems that you can install locally, though they're only no cost if you don't consider your time to be worth anything...

ADD REPLYlink written 6.8 years ago by Gareth Palidwor1.6k

Looks interesting, but prefer a no cost solution.

ADD REPLYlink written 6.8 years ago by Ryan D3.3k
1
gravatar for Daniel Swan
6.8 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

ProjectPier is worth considering, I have used that in projects before, or even something like RequestTracker.

ADD COMMENTlink written 6.8 years ago by Daniel Swan13k
1
gravatar for Gustavo
6.8 years ago by
Gustavo520
Seattle
Gustavo520 wrote:

Other options to consider:

--> http://asana.com

--> http://hiveminder.com

ADD COMMENTlink written 6.8 years ago by Gustavo520
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