Online Bioinformatics Resources

Question

[Eric Normandeau]

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!

Answer 1

[Khader Shameer]

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 : This will come handy when they need to get sequence or other dataset.
• EBI Tools Index: Provides a good preview of various tools from EBI
• BioGPS: 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: 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

[Eric Normandeau]

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

Answer 2

[hadasa]

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. https://www.biostars.org is a great forum for posting questions and not homework!

[Nico]

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

[Paulo Nuin]

Is #2 a recursion?

[hadasa]

y@Nico Corrected it! @nuin :)

[Andrewjgrimm]

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

Answer 3

[Andrew Su]

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.)

[Jeroen Van Goey]

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"

[Neilfws]

Categorically ignoring excel is exactly the answer.

[Michael]

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.

[Andrew Su]

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...

[Eric Normandeau]

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.

[User 59]

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..

Answer 4

[David]

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/

[Eric Normandeau]

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

Answer 5

[Larry_Parnell]

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).

Answer 6

[Michael.James.Clark]

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.

Answer 7

[Mavj]

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

[Mavj]

Which Of The 2011 Nar Database Submissions Are Fully Accessible?