Question: Online Bioinformatics Resources
10
gravatar for Eric Normandeau
9.2 years ago by
Quebec, Canada
Eric Normandeau10k wrote:

Hi,

There seems to be a multiplication of online tool that can be used, within certain limits, to help with bio-informatics. In the context where bio-informaticians are a limited resource and student lab members are often numerous:

What online tools do you think could be used by students to help them be more independent in their projects and analysis, potentially keeping bio-informatics resources for deeper problems?

Ultimately, I will agree with anyone suggesting that they learn to program (R, python, perl...), but I would really like to have your opinion about online tools like, for example, Biomart, Galaxy, or whichever such approaches you have experienced with. What would you recommend?

Thanks!

online • 4.1k views
ADD COMMENTlink modified 8.2 years ago by Michael.James.Clark560 • written 9.2 years ago by Eric Normandeau10k
5
gravatar for Khader Shameer
9.2 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Along with other tools discussed here, I think the following tools will be interesting examples to introduce the availability and scope of tools under various data categories.

Entrez - http://www.ncbi.nlm.nih.gov/sites/gquery : This will come handy when they need to get sequence or other dataset.

EBI Tools Index - http://www.ebi.ac.uk/Tools/ : Provides a good preview of various tools from EBI

BioGPS - http://biogps.gnf.org/#goto=welcome : Provides a quick overview of genes of interested from multiple databases. Can be used to introduce the concept of plugins and ask the students to create their own plugins, layouts etc

PDB Advanced data search - http://www.pdb.org/pdb/search/advSearch.do This is an interesting resource to get structure related data

Array Express or GEO for microarray data mining. Due its simple interface style, I prefer Array Express.

STRING - Known and predicted protein-protein interactions.

ChEMBL or PubChem - to introduce small molecule databases

ADD COMMENTlink written 9.2 years ago by Khader Shameer18k

Thank you for this nice list of resources and the reasons why they are interesting!

ADD REPLYlink written 9.2 years ago by Eric Normandeau10k
4
gravatar for hadasa
9.2 years ago by
hadasa1.0k
hadasa1.0k wrote:
  1. The bioinformatics.org site is a nice information portal and they also host relevant bioinformatics tools and projects like sms2 and others. (http://www.bioinformatics.org)
  2. http://www.biostar.stackexchange.com is a great forum for posting questions and not homework!
ADD COMMENTlink modified 9.2 years ago • written 9.2 years ago by hadasa1.0k
2

I think you mean http://biostarDOTstackexchange.com ;) And I agree it's a nice forum !

ADD REPLYlink written 9.2 years ago by Nico180
2

Is #2 a recursion?

ADD REPLYlink written 9.2 years ago by Paulo Nuin3.7k

y@Nico Corrected it! @nuin :)

ADD REPLYlink written 9.2 years ago by hadasa1.0k

@Paulo: careful there: you might get a Stack Overflow!

ADD REPLYlink written 8.9 years ago by Andrewjgrimm440
4
gravatar for Andrew Su
9.2 years ago by
Andrew Su4.8k
San Diego, CA
Andrew Su4.8k wrote:

DAVID is a nice, user-friendly tool for pathway analysis.

As has been suggested in other question/answers, Biomart/martview is a great tool for identifier translation, another common and annoying "bioinformatics" task.

.. and though it's not trendy, Excel has a lot of uses as a self-serve analysis platform. A basic understanding of formulas will go a long way. (vlookup is by far my most-used function.)

ADD COMMENTlink written 9.2 years ago by Andrew Su4.8k
2

Regarding the use of Excel in bioinformatics, be sure to read the excellent article "Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics" http://www.biomedcentral.com/1471-2105/5/80

ADD REPLYlink written 9.2 years ago by Jeroen Van Goey2.2k
1

Categorically ignoring excel is exactly the answer.

ADD REPLYlink written 8.9 years ago by Neilfws48k

I strongly support Jeroen's comment regarding the use of Excel. We actually teach our students that excel is not an integrative bioinformatics tool. The recommendation of DAVID/BioMart is fully justified in this field.

ADD REPLYlink written 9.2 years ago by Michael Dondrup46k

Point well taken. However, I don't think that categorically ignoring excel is the answer either. Just requires a little training, knowledge, and sanity checking. my two cents...

ADD REPLYlink written 9.2 years ago by Andrew Su4.8k

One of the problems with Excel is that, just as with any other tools, people are not ready to learn it properly. That being said, I try to keep away from it for anything other than visualizing data.

ADD REPLYlink written 9.2 years ago by Eric Normandeau10k

Even today someone got in touch with me who had loaded some analysis I had done for them into Excel (it had not come from Excel ;) and was wondering why their Illumina Probe ID's had turned into dates..

ADD REPLYlink written 8.9 years ago by Daniel Swan13k
4
gravatar for David
8.9 years ago by
David40
David40 wrote:

Have a look to Babelomics. Is nice for microarray analyses and gene set enrichment. It also has a good deal of ready to use database information.

http://babelomics.org/

ADD COMMENTlink written 8.9 years ago by David40

Thanks for the link @david. I'll check it out and I even have a student that could try it now :)

ADD REPLYlink written 8.9 years ago by Eric Normandeau10k
2
gravatar for Larry_Parnell
8.4 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

There is a very nice collection of very basic tools at the University of Massachusetts-Lowell site of bioinformatics.org. Some of their online analysis tools are COMBOSA3D for Molecule coloring, JaMBW for Molecular Biology workbench, PeCoP for Conserved positions, PrimerX for Mutagenic primers, Savvy for Plasmid map drawing, SeWeR for Sequence analysis, Sequence Extractor and SMS2 for Sequence manipulation. The latter offers Format Conversion (e.g. GenBank to FASTA), Sequence Analysis (e.g. DNA Pattern Find), Sequence Figures (e.g. Restriction Map and Translation Map) and Random Sequences (randomization of a sequence).

ADD COMMENTlink modified 8.4 years ago • written 8.4 years ago by Larry_Parnell16k
1
gravatar for Michael.James.Clark
8.4 years ago by
Palo Alto
Michael.James.Clark560 wrote:

As a resource, the SEQanswers forum is very valuable for people in the sequencing space. The Bioinformatics forum there is often one of the most updated sources of information regarding sequence analysis techniques.

ADD COMMENTlink written 8.4 years ago by Michael.James.Clark560
0
gravatar for Mavj
8.4 years ago by
Mavj20
Mavj20 wrote:

This is a good resource, collection of many databases. OBRC: Online Bioinformatics Resources Collection http://www.hsls.pitt.edu/obrc/

ADD COMMENTlink modified 8.4 years ago • written 8.4 years ago by Mavj20

http://biostar.stackexchange.com/questions/4685/which-of-the-2011-nar-database-submissions-are-fully-accessible from Biostar! Link to Nucleic Acid Research database issue.

ADD REPLYlink written 8.4 years ago by Mavj20
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