User: Kraut

gravatar for Kraut
Kraut220
Reputation:
220
Status:
Trusted
Location:
Pittsburgh, PA
Website:
http://www.bleedingedg...
Last seen:
4 years, 4 months ago
Joined:
8 years, 6 months ago
Email:
a*********@gmail.com

2nd hardest working man at BioTeam

Posts by Kraut

<prev • 9 results • page 1 of 1 • next >
1
vote
4
answers
2.3k
views
4
answers
Comment: C: Can Galaxy Be Used Under The Hood? How About The Galaxy Appliance?
... Yes the Galaxy API is enabled on the appliance so you could run workflows from the command-line or a client app. Advanced users can also connect with ssh and submit their own jobs if they wanted to bypass the API. ...
written 5.2 years ago by Kraut220
1
vote
4
answers
2.3k
views
4
answers
Answer: A: Can Galaxy Be Used Under The Hood? How About The Galaxy Appliance?
... The Galaxy Appliance is an open platform and allows you to use the hardware resources however you see fit. To that end we install and configure Sun Grid Engine, specifically opengridscheduler, as the resource manager for galaxy. Jobs submitted through the web will be run through gridengine. Power us ...
written 5.2 years ago by Kraut220
0
votes
20
answers
30k
views
20
answers
Comment: C: Is There A Lims That Doesn'T Suck?
... MiniLIMS now has it's own product page - http://bioteam.net/minilims ...
written 6.8 years ago by Kraut220
3
votes
3
answers
2.9k
views
3
answers
Answer: A: Ab Initio Modelling Of Small Protein
... Rosetta is probably the most widely used program for this problem. It performs very well in many macromolecular modeling problems including Ab initio. You get the software from http://www.rosettacommons.org/. RosettaCommons also has tutorials, examples, and a user forum. The methods have been descri ...
written 7.5 years ago by Kraut220
0
votes
8
answers
4.3k
views
8
answers
Comment: C: In Silico Cell Modelling Platform
... MCell can produce some great visualizations in combination with DREAMM e.g. http://www.youtube.com/watch?v=KQgydF-fXvc ...
written 7.6 years ago by Kraut220
2
votes
1
answer
1.8k
views
1
answers
Comment: C: Are 3D Structures Of Proteins Similar In An Inhibitor Bound State And Unbound St
... Will, you could try removing the ligand form the bound structure and 'relaxing' it with MD or a kinetic framework like Rosetta++. ...
written 7.8 years ago by Kraut220
3
votes
2
answers
2.1k
views
2
answers
Answer: A: Geometric Hashing Of Pdb Structures?
... For comparing PDB structures the first options (in order of sensitivity) that come to mind are: RMSD GDT score TM score These are often used to calculate the similarity between a predicted structure and native native in experiments like CASP. ...
written 7.8 years ago by Kraut220
11
votes
7
answers
3.4k
views
7
answers
Answer: A: How To Think In Parallel In Bioinformatics
... An important part of any parallel programming is thoughtful domain decomposition. In biology you should look for natural parallelism in the objects themselves. For next-generation sequencing, that means parallel by sample, flowcell, tile, or lane. For other problems it's by gene, chromosome, domai ...
written 7.9 years ago by Kraut220
1
vote
4
answers
3.4k
views
4
answers
Answer: A: Downloading Superimposed Pdb Files With Ligand..
... Your best option is to download the structure files from the PDB and use a standalone program like VMD, PyMOL, or JMol. All of them are well suited for this task. There's a classic command-line program called ProFit as well. There may be web services available but you'll ultimately want a visuali ...
written 8.0 years ago by Kraut220

Latest awards to Kraut

Autobiographer 5.1 years ago, has more than 80 characters in the information field of the user's profile.
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: Ab Initio Modelling Of Small Protein
Appreciated 7.9 years ago, created a post with more than 5 votes. For A: How To Think In Parallel In Bioinformatics
Good Answer 7.9 years ago, created an answer that was upvoted at least 5 times. For A: How To Think In Parallel In Bioinformatics
Teacher 7.9 years ago, created an answer with at least 3 up-votes. For A: How To Think In Parallel In Bioinformatics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1504 users visited in the last hour