Free Alternatives To Pipeline Pilot

Question

[Flow]

I got some Pipeline Pilot 8.0 protocols and I wonder if there is some open source or free alternative where I could use them

[Giovanni M Dall'Olio]

it would be easier to answer if you can explain what Pipeline Pilot exactly is and what are you using it for.

Answer 1

[Pierre Lindenbaum]

Some workflow engines in my bookmarks:

• http://www.taverna.org.uk/
• http://www.knime.org/
• https://kepler-project.org/
• Mobyle http://lipm-bioinfo.toulouse.inra.fr/biomoby/PlayMOBY/
• http://www.ailab.si/orange/
• http://ergatis.sourceforge.net/
• ...

EDIT: another one published today: https://conveyor.cebitec.uni-bielefeld.de/Home/About

[Sean Davis]

While not in exactly the same class, there is also Galaxy (http://main.g2.bx.psu.edu/).

[Flow]

thanks for the answer. can any of them import or use somehow pipeline pilot protocols/components?

Answer 2

[Egon Willighagen]

There is also Cyrille2 aimed at genome sequence data annotation workflows.

Answer 3

[Andra Waagmeester]

I don't know pipeline pilot, but I am missing GenePattern from the list of already mentioned workflow systems