Forum: How can bioinformatics tools be grouped/divided into types?
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gravatar for harne.priyanka
2.9 years ago by
harne.priyanka110 wrote:

Hello All,

Background: I am designing a conference for biologists and beginner bioinformaticians to make them understand (simplify) the usage of various bioinformatics tools. However, as I researched more, I found out there are various different types of tools for different forms (genomics, proteomics, drug design, transcriptomics etc.), different applications (drug development, clinical diagnostics etc.) and even further divisions like (gene comparison, gene editing etc.)

My questions: 1) What is the optimal way to divide these tools into types (tracks of conference) so that they are most relevant to the attending biologists and bioinformaticians?

2) To make this event more focused, what is the most important area, you think I should cover (using your experience of working with biologists)?

ADD COMMENTlink modified 2.9 years ago by Emily_Ensembl17k • written 2.9 years ago by harne.priyanka110
2

What you seem to be focusing on are applications of bioinformatics rather than bioinformatics itself. There are methods and there are applications of these methods on specific data and the interpretation of these. Often both are labeled as bioinformatics but that just sweeps the complexities under the rug.

ADD REPLYlink written 2.9 years ago by Istvan Albert ♦♦ 79k

Thanks Istvan, this helps. If I were to divide these tracks based on methods, what are some broad divisions you suggest that will help me deal with the issues faced by them?

ADD REPLYlink written 2.9 years ago by harne.priyanka110
2

Rather than soliciting suggestions from the experts on this forum, wouldn't it make more sense to survey your target audience of potential attendees and ask them what types of information they would find useful?

ADD REPLYlink written 2.9 years ago by harold.smith.tarheel4.3k

Hi Harold, yes that is something that I am doing too. My post here is an attempt to get additional information and learn from different perspectives of experts on the forum. I am still in the planning stage and hence my questions are probably not as specific as required.

ADD REPLYlink written 2.9 years ago by harne.priyanka110
1

What conference are you organizing? Where is the location? Can you add your academic/commercial affiliations to your profile?

ADD REPLYlink written 2.9 years ago by Khader Shameer17k

Hi Khader, since this is just the research/planning phase, I could not share details of when and where this conference is. I am planning it in the US and if I succeed in finding a need for the conference, I will certainly share everything. Also, I will soon add details to my profile, thanks for pointing it out for me.

ADD REPLYlink written 2.9 years ago by harne.priyanka110

If I want to understand how can I divide bioinformatics into types based on methods. Can you suggest any reading resource which can help me understand this?

I am designing tracks for a conference and want to make sure the right content is served in optimally divided tracks.

Thanks for your help in advance!

ADD REPLYlink written 2.9 years ago by harne.priyanka110

Again what conference, which location, who's the organizer?. Please provide full disclosure.

ADD REPLYlink written 2.9 years ago by Khader Shameer17k
1

I guess the OP does not want to reveal the details of the conference unless the design and layout of the conference topics are decided, may be a clause of the company/institution or academic setting where the OP is working. Having said that I can see a lot of topics addressed by Istvan, infact covered the majority of it, I would just like the OP to dig about the usage of NGS technologies in precision and personalized medicine , precisely modeling disease or easing up therapies that could serve for the high end node and later the tree can expand to the different technologies that can actually be exploited for such followed by what kind of exploratory analysis can be employed. The tree can be reversed as well according to the query addressed.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by ivivek_ngs4.6k

IMHO, we all keep the integrity of Biostar by providing our affiliations, this is equivalent of a conflict of interest disclosure in any meaningful scientific engagement. We all are investing the most non-renewable resource we have (time) and it's a courtsey to disclose the affiliations (see the Q&A etiquette by some of the Biostars including myself) know who the OP work for and the commercial/legal affiliations are. We have a diverse set of users on Biostar's and we those who often answers gauge their answers according to the background of the OP. Finally, OP will benefit by providing this information.

I am not happy about supporting an individual/agency that wants to use Biostar as a platform to fish the ideas. Both questions by OP were encouraging the crowd to solve a problem that may have commercial implications and I would definitely request a full disclosure. Let's be open, disclose affiliations and keep on discussing the bioinformatics.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Khader Shameer17k
1

I unanimously support what you say and it is indeed integral part for us to help the community users but then again data mining does give an idea about the OP and it is indeed for commercial usage, having said that I do not discourage the OP to not use the community but yes if its for a commercial use if community has guidelines then definitely relevant disclosure need to be made. I am not sure if this principles are made explicitly outlined while joining Biostars about "it's our right to know who the OP work for and the commercial/legal affiliations", I may not have come across since I was quite sure they were not mandatory fields for joining the community. I am sure certain things can be implemented as of now for making mandatory measures of affiliations. Then it can stand for what you said else I do not see it. The community by and large serves for everyone with potential queries or interest in the field and there was (to my knowledge) no mandate about the affiliations or its commercial use. But yes I echo if it is being used for commercial purpose then certain restrictions can be implemented for benefit of everyone.

ADD REPLYlink written 2.9 years ago by ivivek_ngs4.6k

Thanks - edited the right part... Again, this is my personal opinion. I agree, We have diverse users from all walks of bioinformatics (cores / industry / startup / labs / hospitals / AMC / healthsystem /..). I am not inclined to play the watchdog but we need to do this time and again to ensure that user(s) are not exploiting Biostar to feed predatory conferences/publications. Unless the OP provides an affiliation, we won't be able to validate this.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Khader Shameer17k

Thanks for clearing the airs, am glad that you have brought up this up. I apologize if my tone was a bit harsh , I just did not want to discourage the OP to keep on posting about the field where a discussion on a larger overview of the field might be addressed which can infact be a learning module for newbies in the field. Having said that I completely agree to what you have said and I would really like that people if benefitted from the community should be contributing as well but not use it for commercial purpose, and if used should have complete disclosure of their affiliations. I guess the developers of the community can make the necessary changes in the form of Biostars from now on so that complete disclosure of affiliations are made and if someone is trying to use it for commercial usage then let the community decide how to go ahead with it. Although it is my opinion and anyone can contradict it. And in no way I would want anyone to exploit the community which has contributed so much and every user do it voluntarily at the expense of time. Anyway writing more to this thread would really not be beneficial for both of us and I rest my case. Let the community decide what to do about it and thanks for the discussion.

ADD REPLYlink written 2.9 years ago by ivivek_ngs4.6k

Hello, thank you for your understanding and also making me understand that this may not be the right platform to use for research. I belong to an organization called Markets and Markets which is a market research firm. Please understand that in no way was I trying to disturb this community or discussions here. I thought it is an open discussion forum and I can share and learn more about the industry. However, if my actions here have not been in the right spirit of the community, I sincerely apologize and will refrain from posts like these in future. Hope you will understand, thanks.

ADD REPLYlink written 2.9 years ago by harne.priyanka110

Please pay it forward, once you have enough biostar-points, you will have moderation rights. Take good care of your community.

ADD REPLYlink written 2.9 years ago by Khader Shameer17k
1

Hello Khader, thank you for making me understand that this may not be the right platform to use for research. I belong to an organization called Markets and Markets which is a market research firm. Please understand that in no way was I trying to disturb this community or discussions here. I thought it is an open discussion forum and I can share and learn more about the industry. However, if my actions here have not been in the right spirit of the community, I sincerely apologize and will refrain from posts like these in future. Hope you will understand, thanks.

ADD REPLYlink written 2.9 years ago by harne.priyanka110
1

I think now that the OP made the disclosure and once she updates the profile am sure people can add up more to the discussion but as of now there is enough material for you to dig and understand the need for the conference if it is of use to you. One more important thing is a form of questionaire that you can always make and put it up as a survey , may be not in this community but in other community of social media handles and that might get you a lot of feedbacks. As for the topics discussed there is plenty of material you have as of now.

ADD REPLYlink written 2.9 years ago by ivivek_ngs4.6k

Sure, thanks will work with the information received here.

ADD REPLYlink written 2.9 years ago by harne.priyanka110

Thanks for adding the affiliations.

You are welcome to post your questions, great questions! Bioinformatics is in a rapid transition phase and making great strides with direct application in a clinical setting. Software engineering and application of tools are an important part. To get a comprehensive overview, you may engage some of the experts from the field. Feel free to discuss with some the BioStars as well. All the best wishes with your market research.

ADD REPLYlink written 2.9 years ago by Khader Shameer17k

Thank you for your feedback and for the opportunity to engage with experts in the community. I will discuss with some of them and will keep the community posted on the market research. Will be glad to share the outcome here too!

ADD REPLYlink written 2.9 years ago by harne.priyanka110
3
gravatar for Istvan Albert
2.9 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

The main topics of bioinformatics roughly speaking could be:

  • Biological data repositories: NCBI, ENSEMBL, UCSC
  • Biological data search (BLAST) and visualization (Genome Browsers)
  • Genome/Transcriptome Assemblies
  • Detecting Genomic Variation: SNPs, copy number variation, large scale reorganization
  • Quantification via sequencing: RNA-Seq, ChIP-Seq, RAD seq etc.
  • Making sense of data: Gene Ontology, Pathways Analysis
ADD COMMENTlink written 2.9 years ago by Istvan Albert ♦♦ 79k
1
gravatar for Emily_Ensembl
2.9 years ago by
Emily_Ensembl17k
EMBL-EBI
Emily_Ensembl17k wrote:

The services page from the EBI shows all the categories that the EBI divides its tools/archives/services into. Click into each one to see what's included in each.

ADD COMMENTlink written 2.9 years ago by Emily_Ensembl17k
0
gravatar for Zhilong Jia
2.9 years ago by
Zhilong Jia1.4k
London
Zhilong Jia1.4k wrote:
  1. A workflow for omic data analysis - OMICtools

NAR Database Summary Paper Category List

NAR Web Server Issue

  1. From the users' need (biologists and beginner bioinformaticians) will be great.
ADD COMMENTlink written 2.9 years ago by Zhilong Jia1.4k
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