hit counter joomla

Know your biology!

I get asked often about the type of bioinformatics training that students should get and whether it should be a special course or not.

And I answer that I think teaching bioinformatics in the absence of biology is like teaching Microsoft Word in the absence of writing.

There isn’t much point.

tags: ,

So I was happy, to discover from BioInform, that I’m not the only one who thinks this way.

To quote Lincoln Stein:

I hope to see bioinformatics becoming a tool like molecular biology that everybody uses, and that the software we’re developing now will become as easy and as standard to use as a pipettor. You don’t read for the guy who knows how to run pipettors when you need to pipette something. You reach for the pipettor yourself….

I was even happier to read that some of the most famous people in the field: Lincoln Stein, Russ Altman, Amos Barioch, Rainer Fuchs, Steve Lincoln, and Gene Myers; are also advising students to learn their biology (or as Gene Myers suggested be really good computationalist, and even he says that computer scientists should learn science, too).

(And of course statistics! We all need to know statistics.)

Read the words of the masters in this 10th anniversary edition of Bioinform. They pass on their advice to students and muse about the future of computers and biology.

Comments

  1. #1 Aniesh Joseph
    June 20, 2007

    I agreed Sandra Porter words. As I completed post graduation in Bioinformatics. But our syllabus covered mostly the fundamentals of biology, computer, chemistry and physics. It takes 2 years to cover the basics and nothing more, because the time was over. Now I have a certificate on the latest technology, but could not do anything…

    Someone makes the syllabus, even though they did not heard about the subject and loose the students life.

    I have a suggestion, the government must select candidates for teaching from industry (minimum of 2 or 3 year experience). So they can guide students.

  2. #2 Egon Willighagen
    June 20, 2007

    I can only agree. It’s like biologists who really need to learn their molecular chemistry! Understanding a biological process without understanding the chemistry underneath is just silly.

  3. #3 Animesh Sharma
    June 20, 2007

    The other way to look at it is this, Biology can be a part of the Bioinformatics curriculum. Many of the challenging problems in Bioinformatics can be taught to a computer scientist [and may be a software programmer] in a day or two, For e.g.,
    1. Motif discovery, can be taught as generating a regular expression of given a length with lowest max-possible-string generation from a set of strings of known language
    2. Protein structure prediction from the primary sequence [first principle] is a pure function finding problem which maps them [f(sequence)=structure].

  4. #4 Sandra Porter
    June 20, 2007

    Aniesh: I know exactly what you mean. My answer is here.

    Animesh: You are correct about computer scientists and programmers being able to learn about regular expressions and search for motifs. However, this doesn’t get you very far if you don’t know which motifs you should look for.

    You’re not going to know what makes an important motif without some knowledge of evolution, biology, and biochemistry.

    As far as your second point, we haven’t yet figured out how to predict a final structure from a primary sequence. There’s a contest every year to see who can get closest, and I know that David Baker at the UW does pretty well, but this area of research is still a work in progress. Part of the difficulty is that many structures aren’t determined by the primary sequence alone. Other proteins that assist in the folding and trimming are often involved in creating the final structure.

  5. #5 Larry Moran
    June 20, 2007

    In my experience, the majority of bioinformatics researchers have advanced degrees in the biological sciences and they have learned their computer science on the side, so to speak. This suggests to me that the best advice you can give to students is to learn the biology and find out what the problems are before you start looking for ways to solve them.

    If you learn the tools of bioinformatics first then you’ll be like the proverbial hammer–everything looks like a nail. Either that, or you’ll end up taking directions from biologists instead of running your own lab.

    Our undergraduate program in Bioinformatics and Computational Biology attempts to combine the best of biochemistry and the best of computer science. The results are not encouraging so far. It has mostly attracted computer science students who want additional job opportunities and they really struggle with the biochemistry courses.

    It seems to me that biology and computer science are two different cultures and it may not be possible for undergraduates to succeed with one foot in each culture. That’s the worst of all possible worlds.

  6. #6 Sandra Porter
    June 20, 2007

    Larry: I agree about the culture thing, the programmers that I work with, while smart and creative, have very different phenotypes from the biologists.

    I really think it’s best that students learn how to use bioinformatics tools as part of investigating biological questions and not as an isolated activity. This would be like learning how to use the spectrophotometer – you do learn it better when there’s a purpose.

    I think that all biology and biochemistry classes should be using bioinformatics tools in conjunction with the wet lab.

  7. #7 Larry Moran
    June 22, 2007

    Sandra Porter says,

    I think that all biology and biochemistry classes should be using bioinformatics tools in conjunction with the wet lab.

    We’ve been doing that since 1987 when we first started teaching students how to find sequences in GenBank. Now students learn the basic techniques of BLAST searches and constructing phylogenetic trees in first year biology (if not high school). By second year they are expected to have imaging software installed on their computers and know how to look at protein structures.

    I was recently surprised to learn that some of these tools are only now being introduced into some schools in the USA. What took so long?

  8. #8 Sandra Porter
    June 23, 2007

    Huh! I was in grad school in 1987, using FASTA and GenePro for sequence analysis, we were getting GenBank from a collection of floppy discs, then later on a CD.

    Anyway, I’m in Alaska at the moment and not able to write very much, so we can continue the conversation more, a bit later on.

  9. #9 mahesh sharma
    June 30, 2007

    hi dear me mahesh sharma fm ( INDIA )

    drsharmamahesh@rediffmail.com
    mob no +919868062447 01164545292
    CAREER OBJECTIVE:

    �� Very much Intend to build a career in the field of bioinformatics because I have Qualification of biology with computer , I can play with computer very well & I have to go only and only in the field of Bioinformatics

    PROFESSIONAL QUALIFICATION:

    �Pursuing M.C.A.(4th sem) from Maharshi Dayanand University, Rohtak
    �Completed �A� level in bioinformatics from doeacc society new Delhi

    ACADEMIC QUALIFICATION:

    M.Sc.(3rd sem) in Bioinformatics from sikkim manipal uni.
    �Completed B.Sc. (Microbiology with pharmachemistry) from Davi Ahiya Vishwa Vidyalaya , INDORE
    �Completed Intermediate (Biology group) from M.P.Board INDORE
    �Completed High School from M.P.Board UJJAIN

    Computer Qualification:

    Programming languages: C, java , perl , C++, HTML, visual basic, visual C++, networking, architucher, IT tools,
    Application Software : MS Office 2000

  10. #10 D.V.MANJU NATH
    July 1, 2007

    RESUME

    D.V.MANJUNATH,
    NO: 81, D.G.DODDI,
    DENKANIKOTTA (P.O) & (T.K),
    MAIL : dvmanjunath_bioinfo@rediffmail.com KRISHNAGIRI (D.T),
    MOBILE: 09842399772 TAMILNADU-635107.

    CAREER OBJECTIVE

    To put the best of my ability that I have been obtained through the process of continuous learning and application of analytical skill into the work and flourish in the field to which I belong.
    ACADEMIC PROFILE

     M.Sc in Bioinformatics in K.S.Rangasamy College of arts and science, Tiruchengode under Periyar University with an aggregate of (68% up to III SEM).
     B.Sc in Microbiology at M.G.R college of Arts and science, Hosur under Periyar University with an aggregate of 55%.
     Higher Secondary from Tamilnadu State Board with 43%.
     Secondary from Tamilnadu State Board with 57 %.
    SOFTWARE PROFICIENCY

    Operating System : Windows 98, 2000, XP, MS-DOS

    Languages : C, C++, PERL, HTML

    RDBMS : Oracle 9i
    Package : MS-Office tools

    COMPUTATIONAL BIOLOGY SKILLS

    BIOLOGICAL DATA BANKS : NCBI, PDB, EMBL, SWISS PROT, PIR, DDBJ & CSD, PMD.
    BIOLOGICAL TOOLS : BLAST, FASTA, Clustal W, Emboss, Prosite, pfam, power.

    BIOLOGICAL SOFTWARE?S : RASMOL, PYMOL, SWISS-PDB, CHEM site, VECTOR
    NTI, HEX, EXPRESSION.

    MINI PROJECT:
    Bioinformatics tool development on ?TRANSLATION IN DIFFERENT ORGANISMS? using CGI-Perl and html.
    PROJECT WORK:
    Title: ?COMPUTATIONAL ANNOTATION ON GENETHERAPY OF OCD (SLC6A4)? in BTIB TECHNOLOGIES PVT LTD in Bangalore.

    ADDITIONAL QUALIFICATION:
    Advance Diplomo in software application.
    OTHER ACTIVITIES:
     Fifth National level biological congress on ?Biotechnology: A global perspective?in muthayammal college of arts and science.

     Industrial visit on Indian institute of science, Bangalore.

     Project Training at BTIB Technologies (p) ltd, Bangalore.

    PERSONAL DETAILS:
    Name : D.V.MANJUNATH,
    Father?s Name : Mr.D.M.VENKATASWAMY,
    Date of Birth : 03 – 06 – 1981
    Sex : Male
    Marital status : Single
    Nationality : Indian
    Permanent Address : No: 81, D.G.Doddi,
    Denkanikotta Post and T.k,
    Krishnagiri (D.T),
    Tamilnadu -635107.
    Mobile No : 09842399772
    Contact phone : 04347-235568
    LANGUAGES KNOWN:

    Read Write Speak
    English
    Tamil
    Telugu
    Kannada

    DECLARATION

    I hereby declare that the details furnished above are true to the best of my knowledge.

    Date:
    Place: Denkanikotta.

    (D.V.MANJUNATH)

    REFERENCE:

    1. Dr.Kannan,
    Director,
    KSR College of Technology,
    Tiruchengode.

    2. Mr. Muthu kumaran ,
    H0D Dept of Bioinformatics,
    K.S.R. College of Arts and Science.
    Tiruchengode.

    3. M.S.Yatnatti, CEO
    BTIB Technologies (P) Ltd,
    Bangalore.

  11. #11 sonali
    July 3, 2007

    i m post graduate in genetics n have done post graduate diploma in bioinfprmatics.i have done summer project on dock in jnu delhi.i have limited practical exposure in field becoz of which unable to get job as researcher.kindly suggest online certificate programs for practical in bioinformatics.plz help.

  12. #12 Sandra Porter
    July 3, 2007

    Hi Sonali and company,

    I wish I could help, but I don’t know much about certificate programs in India or elsewhere for that matter. I’m suprised that you could get a post graduate degree in genetics, these days, without doing some bioinformatics during your research project.

  13. #13 trimurthy.n
    September 7, 2007

    Hi, i am trimurthy post graduate in M,Sc- Biotechnology,from bangalore university,i need a better job in a biotech industry can any one help me.

    with Rgds,
    trimurthy.n
    banglore.

  14. #14 Sandra Porter
    September 7, 2007

    The first question I think you need to answer is this:

    What do you consider a “better job”?

  15. #15 kaavya
    July 23, 2008

    hi dis s kaavya doin b.tech bioinformatics in chennai i wud like to do my project in btib tech so can u jus send me the formalities for the same.thanks

  16. #16 Mahesh Sharma
    September 30, 2008

    Dear Sir,

    My name is Mahesh Sharma, with this letter; I request to reconsider me for the recruitment.

    As the world constantly demands more specific biological data at faster speeds, manufactures are racing to supply the equipment to make it possible. All of this is possible only due to Bioinformaticion, which involves lots of biological process. The organization of Biological data and Analysis lead the R&D industry into the Bioinformatics.

    My M.Sc. (Bioinformatics) work is on the Data Base for Bioinformatics & Computing, Biological System & Bioinformatics, Windows Application, MS-Office, HTML, Multimedia, Static & Probability, Computational Method for Sequence Analysis, Biological Data Bank & Analysis, (OOPS), Perl for bioinformatics, VB, Drug Design &Gene Therapy, Plant Genomics, JAVA, Photoshop, Flash, Dream Weaver, Data Warehousing & Data Mining, Numerical Method & Optimization Tech, Emerging areas in Bioinformatics.

    Before this I did B.Sc. in microbiology+pharmachemistry. In M.Sc. My project work was Pharmacophore Modeling in LEUKEMIA Diseases. After the analysis of Leukemia we have Identified a genetically linked gene which is responsible for Leukemia.(ABL1 chro-9),(AFF1 chro-4), (MKL1 chro-22) from gene we find out some interest Protein which have more than four ligand (Pro-2FO0 ,lig:-MYR1, P162, SEP69, GOL3, GOL4), (Pro-2G1T, Lig:- 1121202, -101, 401, GLU105, GLU104, GLU111), (Pro-2GQG, Lig:- 1N1501,PTR393-A,B,GOL1), (Pro-2HYY, Lig:- STI600-A,-B,-C,-D) Than find Out Best suitable Pharmacophore Model with the help of Ligandscout 1.03 Tool. In a Result if any Drug fully binding with this Pharmacophore so we have 100% Treatment of LEUKEMIA. For This Experiment I refer to NCBI, TIGR, EBI, HPRD, SWISS-PROT data base

    My knowledge in Bioinformatics, familiarity with experiments and advance knowledge in Computer Aided Drug Designing, Molecular Modeling, Computational Biology, Immunology, Recombinant DNA Technology, Genomics & Proteomics, Metabolic pathways, Gene Sequence Analysis, Protein Sequence Analysis, Discovery of genuine drugs for LEUKEMIA using Bioinformatics Tools, Phylogenetic Analysis, Virtual Screening and Docking. Motivate me to pursue a career in this field.

    Please find the resume attached.

    Yours Sincerely
    Mahesh Sharma
    M.Sc. Bioinformatics
    B.Sc. Microbiology + Pharmachemistry
    +91-9868062447 +91-9910045441
    E-mail: drsharmamahesh@rediffmail.com

    MAHESH SHARMA

    ADDRESS:
    A-133a New Ashok Nagar
    Delhi-110096

    OBJECTIVE

    To be a part of professional organization where I could apply and hone my acquired skills and to work the fullest of my potentials and knowledge in a challenging and intellectually stimulating environment in the field of Bioinformatics.

    EDUCATIONAL QUALIFICATION

    � M.Sc, 2008 (Bioinformatics) from Sikkim Manipal University.
    � B.Sc, 2005 (microbiology+pharmachemistry) from Maharaja Ranjit Singh College. DAVV � INDORE
    � 12th , 2001 from SVH School � INDORE (M.P. Board)
    � 10th ,1998 from Govt. H school � Ujjain (M.P. Board)
    PROFESSIONAL QUALIFICATION:

    � DOEACC �A� level (PG-Level) in Bioinformatics Delhi. (A unit of DOEACC Society, An autonomous body of Deptt. of Information Technology, Ministry of Communications & Information Technology, Govt. of India)

    SUBJECTS STUDIED

    Bioinformatics:-
    Data Base for Bioinformatics & Computing, Biological System & Bioinformatics, Windows Application, MS-Office, HTML, Multimedia, Static & Probability, Computational Method for Sequence Analysis, Biological Data Bank & Analysis, (OOPS), Perl for bioinformatics, VB, Drug Design &Gene Therapy, Plant Genomics, JAVA, Photoshop, Flash, Dream Weaver, Data Warehousing & Data Mining, Numerical Method & Optimization Tech, Emerging areas in Bioinformatics.
    Pharmachemistry: -
    TLC, HPLC, GLC, paper chromatography & column chromatography. Drugs preparation: – syrup, lotion, Drops crystallization. Drugs activity, QSAR, MM, ADME, IP, BP, Body Receptor, Na, K, Mg,-Channels, Chemical Isomerism.
    Microbiology:-
    Soil Microbiology, Food Microbiology, Water Microbiology, Waste Water Treatment, Air Microbiology, Fundamentals of Genetics, DNA Replication and Gene Structure, Mutation, Genetic Recombination, Infection, Immune System , Immune Response, Antigens and Antibodies, Antigen and Antibody Reactions, Fundamentals of Industrial Microbiology, Fermentor Design, Scale up, Industrial production, Bioassays, Quality Cont, Colorimetry and Spectrophotometry, Separation Techniques, Microorganisms in Agriculture, Geomicrobiology, Pharmaceutical, Biotechnology, Food from Microbes, Advanced Microbiology, Regulation of Gene Activity, Genetic Engineering, Gene Cloning, Techniques in Molecular Biology, Applications and Biohazards of Genetic Engineering
    Experimental Microbiology:-
    Isolation of microorganisms by Sector Plate/Pour plate method, Differential staining, Special staining, Isolation of microorganisms from water / sewage / food / curd / canker/soil, Qualitative estimation of carbohydrates / proteins / lipids, Total count of RBC/WBC/Differential count of WBC/Hb estimation, Antigen-antibody reactions � Widal /VDRL, Isolation of mutants by replica plating technique/gradient plate technique, Identification of medically important organisms Staphylococcus / Streptococcus, E.coli , Urine analysis / Antibiotic sensitivity testing / Gradient Plate Technique, Qualitative and Quantitative analysis of water/food/milk/sewage, Microbial assay of Antibiotics/ Isolation of industrially important microbes/Paper Chromatography/TLC, Isolation of bacterial/fungal DNA, Quantitative estimation of DNA/RNA, Isolation of Rhizobium

    PROJECT & WORKSHOP

    � Pharmacophore Modeling in LEUKEMIA Diseases. After the analysis of Leukemia we have Identified a genetically linked gene which is responsible for Leukemia.(ABL1 chro-9),(AFF1 chro-4), (MKL1 chro-22) from gene we find out some interest Protein which have more than four ligand (Pro-2FO0 ,lig:-MYR1, P162, SEP69, GOL3, GOL4), (Pro-2G1T, Lig:- 1121202, -101, 401, GLU105, GLU104, GLU111), (Pro-2GQG, Lig:- 1N1501,PTR393-A,B,GOL1), (Pro-2HYY, Lig:- STI600-A,-B,-C,-D) Than find Out Best suitable Pharmacophore Model with the help of Ligandscout 1.03 Tool. In a Result if any Drug fully binding with this Pharmacophore so we have 100% Treatment of LEUKEMIA. For This Experiment I refer to NCBI, TIGR, EBI, HPRD, SWISS-PROT data base
    � Fully Working Fermentor Model Design. In which we can incubate Org. Put antifoaming agent, and have impeller to rotated, Use Home 220 volt current, Apply Temp, capacity 2 liter only. In a final Project of B.Sc. Microbiology.
    � Participant of workshop in G.B.Pant University (Uttarakhand) �Biological sequences analysis and application in crop improvement� Nov16-17,2007
    � Develop an Offline Web site For DOEACC. In Final Project.
    � Six month Training on DOTNET at Alien SoftNet Technologies Pvt. Ltd.
    TECHNICAL SKILLS

    Language: – DOTNET, C, C++, VB, PERL, Core Java, HTML, XML, Networking.
    OS: – window 98, 2000, XP. Linux.
    Database: – SQL- server 2000, SQL- server 2005.

    BIOINFORMATICS SKILLS

    Bioinformatics tools: BLAST, FASTA, Ligandscout 1.03, T-COFFEE, CLUSTAL-W, cn3d, Geneious 2.5.2.
    Databases: NCBI, TIGR, EBI, HPRD, ENTREZ, EMBL, GENBANK, SWISS-PROT, ICTV MetaCyc, EcoCyc, KEGG.

    AREA OF INTEREST

    Software developer in DOTNET Technology
    Computer Aided Drug Designing, Molecular Modeling, Computational Biology, Immunology, Recombinant DNA Technology, Genomics & Proteomics, Metabolic pathways, Gene Sequence Analysis, Protein Sequence Analysis, Discovery of genuine drugs for Cancer using Bioinformatics Tools, Phylogenetic Analysis, Virtual Screening and Docking.

    PERSONAL PARTICULARS

    Mahesh Sharma
    24-01-1984
    Satyanarayan ji Sharma
    Laleeta ji Sharma
    Indian
    Male
    Single
    English, Hindi
    Net Browsing & Traveling, making fn.
    191- Sharma Niwas Junashar BARNAGAR , Dist- Ujjain (M.P.) (INDIA)
    (+91) (7367) 225952 , 262111

    DATED: SIGNATURE
    PLACE:

The site is currently under maintenance and will be back shortly. New comments have been disabled during this time, please check back soon.