BIOINFORMATICS FACILITIES WITH C-DAC

(This blog post sums up details given at official site of Bioinformatics, C-DAC http://bioinfo-portal.cdac.in/. For more details, latest updates and verifications, please refer to the official portal. This is just to share the world class facilities available with the organization for researchers in different areas of Bio-Technology.)

Centre for Development of Advanced Computing (C-DAC) is the premier R&D organization of the Department of Electronics and Information Technology (DeitY), Ministry of Communications & Information Technology (MCIT), Government of India for carrying out R&D in IT, Electronics and associated areas.

A.   BIOINFORMATICS RESOURCES & APPLICATIONS FACILITY (BRAF) by C-DAC

 

              I.        INFORMATION ON BRAF

 

This blog post refers to the details given at - http://bioinfo-portal.cdac.in/braf.html

  

            II.        BRAF COMPUTING RESOURCES

·         BIOGENE - supercomputing environment

 

·         BIOCHROME - advance blade server based HPC facility

 

·         BIOBANK - data Storage solution

 

·         NGS Server - high memory CISCO UCS 450 server having 512 GB RAM and 32 computing cores

 

·         Hardware Acceleration using RCS Card

 

           III.        APPLICATION SOFTWARES ON BRAF

·         Sequence Analysis: FastA,BLAST, ClustalW, MEME, Phylip, AlignACE, cross match, EMBOSS, RAxML, Elph, Weeder , Primer3 , Seqclean , SIGNALP , Prophage, Mutual information

·         Molecular Modelling: AMBER, CHARMM, GROMACS, Sybyl, Accelrys NAMD

·         Ab-initio methods: MOPAC, GAMESS, Gaussian

·         Biomolecular Docking: DOCK6

·         Microarray Data Analysis: Cluster

·         Gene Finding Algorithms: TMHMM, Genscan, Glimmer, Prodigal

 

·         Genome Alignment: MUMMER, MGA, LAGAN, mauve, Murasak

 

·         Repeat finding tools: mRep, Phobos, repeatMasker, TRF, tandemscan

 

·         RNA analysis algorithm: RNAmmer, tRNAscan, Vienna RNA

 

          IV.        SOFTWARE LICENSES

 

Following Molecular Modelling facilities need licenses:-

·         The Amber license Agreement is a legal agreement between the end user (either an individual or an entity) and the University of California.

o   AMBER : Users who wish to use AMBER should adhere and follow AMBER License as given in below Link.

o   License : http://ambermd.org/amber11.license.html

 

·         Academic users can obtain CHARMM by contacting The CHARMM Development Project. For-profit companies should contact Accelrys Inc.

o   CHARMM : Users who wish to use CHARMM should adhere and follow CHARMM License as given in below Link.

o   License : http://www.charmm.org/package/license.html

           V.        BRAF ACADEMIC REGISTRATION FORM

 

·         Available at - http://bioinfo-portal.cdac.in/braf_forms/RegistrationForm_Academics.pdf

·         The complete registration form should be faxed to 020-25694084

 

·         For any queries, users can send an email to braf-help@cdac.in

 

          VI.        ACCESS FOR INDUSTRIAL USERS

BRAF is accessible to industrial users on case to case basis and in the mode of contract research projects.

B.   OTHER BIOINFORMATICS FACILITIES (or PRODUCTS) by C-DAC

Some other Bio-Informatics facilities (or Products) with C-DAC are as under:-

 

                      I.        ANVAYA - Workflow Environment for high-throughput genome analysis - (Reference - http://bioinfo-portal.cdac.in/anvaya.html )

Comprehensive analysis of heterogeneous genomic data requires a flexible platform for running complex queries that is capable of integrating and analyzing large amount of genomic data in pipeline.

Anvaya Distribution and Usage:-

·         Free Download Client Installer is available at the site.

·         The client will interact with pre-installed server on C-DAC's BRAF facility (In the downloaded client, ensure Server and Proxy settings are properly done)

·         Kindly Register for dedicated login account. For trial purpose use guest account (login: guest, password: gue2Anv)

·         Login account will be valid for 6 months duration by default and may be extended on further request

 

                    II.        MORE C-DAC Products for BIO-INFORMATICS can be accessed at:-

http://bioinfo-portal.cdac.in/products.html

FOLDIT - AN INNOVATIVE WAY

Protein Folding Problem of Scientific Community in a Computer Game

 

Change in shape of the proteins attribute to biochemical explanation of biological functions. May it be understanding different pathways (series of biochemical reactions) or may be understanding the nature of virus attack, the way the proteins change shape play critical role. Therefore, understanding of protein structure is important for biologists. But, at the same time, it is an extremely complicated task. Further, to simulate the change in the shape of proteins in a dynamically changing environment is a much more difficult task. Today, researchers across the world are trying to achieve perfection in understanding behavior of shapes of proteins (commonly referred as 'Protein Folding Problem').

On the web, there is a protein folding game called Foldit with real protein sequences in three dimensions. Foldit was developed by a large group of researchers who are interested in protein folding. Interestingly, at times humans have done better in folding proteins than computers. This is an innovative move in the area of computer games. The real problems of science would be attempted by zealous community interested in computer games.  

Further details on 'The Science Behind Foldit' can be accessed at:-

http://fold.it/portal/info/about

Foldit can be downloaded from the following website:-

http://fold.it/portal/

Frequently Asked Question on Foldit website are given in the following web page:-

http://fold.it/portal/info/faq

FolditForum

http://fold.it/portal/forum/5

List of the players of Foldit with profiles are listed in the web page:-

http://fold.it/portal/players/profs

In the above link (listing profile of the players), it can be observed that passionate minds are coming from cross-functional background to play Foldit. Probably, this is a dream come true for intellectual community. Success of the promising game (Foldit) may encourage the portal management to innovate with other possibilities to attract more and more passionate people from all walks of life. In the present form, the portal may help in promoting researchers in remote and underdeveloped areas to network and contribute at international level. Let us wish all the very best to Foldit.

BITians HAVE GOT PLACED IN REPUTED ORGANIZATIONS ACROSS DIFFERENT INDUSTRIAL SECTORS - ANALYSIS OF BIT ALUMNI DATA

(Please click on the pictures to view as slide show)

picture - 1 

 

picture - 2 

 

picture - 3

(Please find much detailed data sheet in the section - Analysis Documents) 

 

 

picture - 4

(Please find much detailed data sheet in the section - Analysis Documents)

 

Reference to Previous Blog Post

In the blog post MANAGEMENT OF HUMAN RESOURCE FOR INVESTORS IN KOWLEDGEBASED INDUSTRIES IN CHHATTISGARH

(paragraph-2, point 1), it has been suggested that talented fresh graduates from local institutions could be groomed to work in knowledge based companies of national and international repute. In this blog, an attempt has been made to figure out whether the locally reputed educational institutions (in Chhattisgarh) have been successful in offering quality resources to industries across different industrial sectors. To have a very broad idea on this topic, we have chosen to do an analysis of alumni data of one of the premier institution of the state BIT (Bhilai Institute of Technology), Durg.
 

Source of Data - http://www.bitdurg.org/alumni/seeall.asp as accessed last on 25 OCT 2012.
 

Objective of Analysis

To get a broad idea on how students passed out from any premier institute (for example BIT, Durg) in Chhattisgarh have (in general) got placed? The analysis is carried out using data publicly available at the Alumni section in website of BIT Durg (http://www.bitdurg.org/alumni/seeall.asp)

Brief on BIT (Bhilai Institute of Technology), Durg

1.    One of the premier institutions in Central India

2.    Established in 1986

3.    Affiliated to Chhattisgarh Swami Vivekanand Technical University

4.    AICTE approved Institution

5.    Accredited by National Bureau of Accreditation 

6.    ISO 9001-2008  Certified Institute

7.    Accredited by Tata Consultancy Services

8.    Official Website - http://www.bitdurg.org

9.    WIKI - http://en.wikipedia.org/wiki/Bhilai_Institute_of_Technology_%E2%80%93_Durg

 

Limitations

1.    The data available at the mentioned website does not represent the complete data of all the alumni of BIT, Durg. This data only reflects details of some of the alumni who have updated details in the website.

 

2.    The data at the above mentioned website may not necessarily be showing the latest detail of each alumnus. It may be reflecting the details of the alumni as per the point of time respective alumnus have last filled their details on the website.

3.    It is assumed that all the valid data given in the website are real data correctly filled by alumni.

 

4.    On viewing the data it seems that the ‘Batch’ has been interpreted in different ways by BIT alumni. While most alumni have considered their year of passing out from BIT as their Batch, a few of the students have considered their year of admission to BIT as their Batch. However, this doesn’t make much difference for the objective of this analysis.   

 

5.    Alumni, who have mentioned their company/organization as academic institution (like IIT, IIIT, BIT, etc.) may either be working in these organization or may be pursuing further studies / researches.

 

6.    Industrial Sectors / Domains specified in this analysis may not be as per any formal convention. This classification has been done for ease of analysis. Companies/Organizations are classified based on the details of the organizations given in the websites.

 

Acknowledgements

1.    We are grateful to Dr. M.K. Kowar, Director, Bhilai Institute of Technology for extending all the possible help for this work.

 

Conclusion

Considering BIT to be representative institution in Chhattisgarh, it could be assumed in general, that alumni in institutions of Chhattisgarh have got placed in reputed organizations across different industrial sectors / domains.

 

Disclaimer

All care has been taken to ensure that the information listed is correct. However because of nature, some information might have changed or some data may have lost during data refining / data analysis. Visitors are advised to research independently. www.santoshbehar.blogspot.in shall not have any responsibility in this regard.

 

Analysis Documents

Exported Data from website - http://www.bitdurg.org/alumni/seeall.asp is given in the following sheet:-

https://docs.google.com/file/d/0BwOOneTw-vSdZG90LVF2ekQtREk/edit?usp=sharing

Analysis of Data from website - http://www.bitdurg.org/alumni/seeall.asp as used in this blog post are detailed in the following sheet:-

https://docs.google.com/file/d/0BwOOneTw-vSdT0dDZ3FMZ0xVS1E/edit?usp=sharing 

Analysis Team

  Santosh Behar                                                                                      Vikas Mishra

  Neha Behar

A COUPLE OF POINTS FOR PRACTIONERS OF SOCIAL MEDIA FRAMEWORK

 (CONTEXT: Framework & Guidelines for Useof Social Media for Government Organizations, Department of Electronics andInformation Technology, Government of India)

‘Framework and Guidelines for the use of Social Media’ addresses all the aspects on this subject in great detail. However, for practitioners, it may become easier to work out with the six elements of the framework, if the following two very closely related areas are taken into account:-

a)      Design of Information Management (for the organization) and

b)      Building Capacity for Formal Communication (within the organization)

In fact, these two areas can become a two layered platform (with Design of Information Management being the base layer), on the top of which, the six elements of the framework can be placed.  In this way, the pictorial representation of the framework (Figure 2 in the document ‘Framework and Guidelines for the use of Social Media’) may get modified for practical implementation as shown in the figure below:-

 

 

Source – Figure 2 of Framework and Guidelines for the use of Social Media (http://deity.gov.in/sites/upload_files/dit/files/Approved_Social_Media_Framework_and_Guidelines.pdf ) – Modified by Author to illustrate how practitioners can use the framework for ease of implementation.

 

Brief on the areas are given below:-   

a)      Designing Information Management

For use of social media as an information channel, a smooth information management with clear understanding of information and its significance within an organization is required. Even though designing information management is a complex matter and is linked to organizational design, in general, following could be important points:- 

1)      Classification of Information

An analysis of information with respect to various parameters (like criticality, target, and confidentiality) related to generation, propagation and consumption of information may lead to Classification of Information for an organization. Statistical analysis of historical data could be useful in understanding organizational data from different aspects and hence would help in the classification efforts.  

2)      Design of Information Flow

Clear Information Flow paths based on organizational design with well defined information access criteria can be helpful in ascertaining integrity of information. Generally, government organizations have a defined mechanism for information flow. A review (and may be re-engineering) on the same in the light of modern communication medium could be helpful.

3)      Version Maintenance of Informative Documents

Accessibility of version maintained documents to authorized persons will help in coherence in information across the department.

4)      Information Management Audit

Audit of Information Management for a department will help in ensuring availability, accessibility and integrity of information in a department.

b)     Building Capacity for Formal Communication within Organization

It needs training and proper understanding to imbibe practice of sensible, responsible, concise and clear communication through different medium of written and verbal communications. Capacity Building for the same has to become an integral part of efforts on Human Resource Development and Induction Training.

Confident work force with thorough understanding of information design (of the organization) along with their roles and responsibilities (with respect to information and information flow) will be able to use social media for government organizations in the best possible way. 

 

Thus, if the organization has a pre-existing document on ‘Design of information Management’ this could be taken as an input for implementing the Social Media Framework. If there is no such document, working out a very basic design could be considered for the purpose of simplifying implementation of the framework. In particular, such an effort will be helpful in relation to following elements of the framework:-

• Objective
• Governance
• Communication Strategy

Similarly, if the organization has skill development programs targeted at developing skills for Formal Communications across different media, an inclusion of social media would prepare the workforce for the new challenge. In case, the organization does not have such skill development programs in place, sensitization and capacity building on the same may be required at all levels. A thorough understanding on information management within the department would be helpful in relation to following elements of the framework:-

• Governance
• Institutionalization

 

REFERENCES:-

http://www.medianama.com/2012/08/223-indian-govt-releases-social-media-guidelines-for-its-agencies-highlights/

http://deity.gov.in/sites/upload_files/dit/files/Approved_Social_Media_Framework_and_Guidelines.pdf

 

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RESULTS-SURVEY–1: IS CHHATTISGARH READY TO BRING HOME PROFESSIONALS WORKING AWAY?

BACKGROUND:

Background to the Survey is given in the following blog-post:-

MANAGEMENT OF HUMAN RESOURCEFOR INVESTORS IN KOWLEDGE BASED INDUSTRIES IN CHHATTISGARH

SURVEY DESIGN:

Document on the Design of the Survey can be accessed at following link:-

DESIGN – SURVEY–1: ISCHHATTISGARH READY TO BRING HOME PROFESSIONALS WORKING AWAY?

SURVEY RESULTS

In the survey, professionals from the state working at different locations across the globe were asked to make choice on following questions:-

Question-1: With good institutes getting operational (like IIM, IIIT, AIIMS, HNLU), improved health care facilities, improving recreational facilities (Malls and Multiplexes, Open-Air Museum, Stadiums), enhanced connectivity, availability of residential societies with best amenities and with attitudinal support for multicultural harmony, do you think that now Raipur is one of the happening places?

To select answers from following choices:-

a.     Strongly Agree

b.    Agree

c.     Disagree

d.    Strongly Disagree

e.    Can't Say

Question-2: Would you like to relocate to Raipur, if you are offered the same job profile with same pay package and same career development path by your company (or any other company at par with the company you work for)?

To select answers from following choices:-

a.     Surely

b.    May be

c.     May be after a few years

d.    No

e.    Never

f.      Can't Say

 

In reference to Question-1 and Question-2 above, the key results of the survey are summarized in the following paragraphs.

Professionals having their home towns in the state of Chhattisgarh have shown a strong inclination in favor of relocating to work in the state. In the survey, approximately three fourth (74.3%) of the respondents have indicated that they would ‘Surely’ like to return to Chhattisgarh.

Further, 32.4% of the respondents ‘Strongly Agree’ and 47.1% respondents ‘Agree’ that Raipur (Capital City of Chhattisgarh) is now amongst the happening places in India. Among these respondents (who either ‘Strongly Agree’ or ‘Agree’ that Raipur is a happening place), 83.8% have indicated that they will like to relocate to Raipur and only 2.5 percent have indicated that they would not like to relocate to Raipur.

Interestingly, approximately half of the respondents (46.7%) who did not agree (opted for ‘Strongly Disagree’, ‘Disagree’ or ‘Can’t Say’) with the fact that Raipur is now a happening place, have also indicated that they would ‘Surely’ like to relocate to Raipur, if offered job prospect at par with their current job. However, one fifth (20%) of such respondents indicated that they would not like to relocate to Raipur.

78.8% of respondents in the age group of 20-29 years have marked ‘Surely’ against 65.7% of respondents in the age group of 30-49 years, while answering for the question on relocation to Raipur. Further, for the same question, 78.8% of males were sure (marked ‘Surely’) as against 60% females (who marked ‘Surely’). On the contrary, in the response to question on Raipur being a happening place, respondents were more or less consistent across age-group and gender (with percentage of respondents answering ‘Strongly Agree’ lying in the range of thirties, while those answering ‘Agree’ lying in the range of forties).

On the question of relocation, 66.7% of married respondents answered ‘Surely’ as against 83.7% of the respondent having marital status as Not Married (Never Married, Separated, Divorced and Widowed). Similarly, among the respondents having no kids, 76.3% responded to the question (on relocation) with answer choice of ‘Surely’ against 65.2% of those having kids. Further, amongst those respondents who have kids, the group of respondents having eldest kid in age-range 0-5 were more open to relocation (78.6% have indicated ‘Surely’ through answer choices for question on relocation) in comparison with the group of respondents having eldest kid in age-range >5 years (only 44.4% have indicated ‘Surely’ through answer choices for question on relocation).

77% of respondents working in services sector opted for ‘Surely’ as answer to question on relocation, while 71% from other sectors (other than services sector) have responded the same question with ‘Surely’. On question related to Raipur being a happening place, around 80% in both these categories have either chosen ‘Strongly Agree’ or chosen ‘Agree’.

Marginal differences were observed with respect to locations as well, as (in response to question on relocation to Raipur) 64% of respondents working abroad indicated ‘Surely’ against 77% respondents working in India. Similarly, 78% of the respondents, who hail from Raipur showed their eagerness to come home by selecting ‘Surely’ for question on relocation to Raipur and 71% of those respondents who have their home towns located in cities other than Raipur have selected ‘Surely’ for the same question.

On taking a conservative approach, the ratio of the respondents who agreed to Raipur being a happening place to those who disagreed for the same has been found to be 3.69 (amongst all the respondents). In this ratio calculation extreme answer choices (‘Strongly Agree’ and ‘Strongly Disagree’) and indecisive answer choice (‘Can’t Say’) have not been considered.

 

More details on the results of the survey are available at following links:-

RESPONDENT DISTRIBUTION

(Important Graphs on Respondents Distribution are listed below the blog for your reference)

More details on Respondents Distribution can be accessed at following link:-

RESULTS– RESPONDENTS DISTRIBUTION FOR SURVEY–1: IS CHHATTISGARH READY TO BRING HOMEPROFESSIONALS WORKING AWAY?

 

SURVEY RESULTS

(Important Graphs on Survey Results are listed below the blog for your reference)

More details on Survey Results can be accessed at following links:-

 

DETAILED-RESULTS–SURVEY–1: IS CHHATTISGARH READY TO BRING HOME PROFESSIONALS WORKING AWAY?

 

TABULAR-RESULTS–SURVEY–1: IS CHHATTISGARH READY TO BRING HOME PROFESSIONALS WORKINGAWAY?

SURVEY TEAM:

Santosh Behar                                                                                                 Abhijit Chakravarty

Neha Behar                                                                                                      Abhishek Agrawal 
 

- - - - - - - - - - - - - - - - - - - -

 

 

RESPONDENT DISTRIBUTION

(CLICK AT IMAGES TO ENLARGE AND VIEW AS SLIDES)



 

 

 

KEY SURVEY RESULTS

(CLICK AT IMAGES TO ENLARGE AND VIEW AS SLIDES)

 

 

OVER ALL RESPONDENTS

 

 

 

OTHER IMPORTANT RESULTS

 

 

 

 

 

 

 

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