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BIOINFORMATICS ORIGINAL PAPER Vol. 27 no. 22 2011, pages 3149–3157 doi:10.1093/bioinformatics/btr546 Systems biology Advance Access publication September 29, 2011 TFRank: network-based prioritization of regulatory associations underlying transcriptional responses Joana P. Gonçalves 1,2, , Alexandre P. Francisco 1,2 , Nuno P. Mira 3,4 , Miguel C. Teixeira 3,4 , Isabel Sá-Correia 3,4 , Arlindo L. Oliveira 1,2 and Sara C. Madeira 1,2,1 Knowledge Discovery and Bioinformatics group, INESC-ID, 2 Department of Computer Science and Engineering, Instituto Superior Técnico (IST), Technical University of Lisbon, 3 Institute for Biotechnology and Bioengineering, IST, Technical University of Lisbon and 4 Department of Bioengineering, IST, Technical University of Lisbon, Lisbon, Portugal Associate Editor: Alfonso Valencia ABSTRACT Motivation: Uncovering mechanisms underlying gene expression control is crucial to understand complex cellular responses. Studies in gene regulation often aim to identify regulatory players involved in a biological process of interest, either transcription factors coregulating a set of target genes or genes eventually controlled by a set of regulators. These are frequently prioritized with respect to a context-specific relevance score. Current approaches rely on relevance measures accounting exclusively for direct transcription factor–target interactions, namely overrepresentation of binding sites or target ratios. Gene regulation has, however, intricate behavior with overlapping, indirect effect that should not be neglected. In addition, the rapid accumulation of regulatory data already enables the prediction of large-scale networks suitable for higher level exploration by methods based on graph theory. A paradigm shift is thus emerging, where isolated and constrained analyses will likely be replaced by whole-network, systemic-aware strategies. Results: We present TFRank, a graph-based framework to prioritize regulatory players involved in transcriptional responses within the regulatory network of an organism, whereby every regulatory path containing genes of interest is explored and incorporated into the analysis. TFRank selected important regulators of yeast adaptation to stress induced by quinine and acetic acid, which were missed by a direct effect approach. Notably, they reportedly confer resistance toward the chemicals. In a preliminary study in human, TFRank unveiled regulators involved in breast tumor growth and metastasis when applied to genes whose expression signatures correlated with short interval to metastasis. Availability: Prototype at http://kdbio.inesc-id.pt/software/tfrank/. Contact: [email protected]; [email protected] Supplementary Information: Supplementary data are available at Bioinformatics online. Received on March 23, 2011; revised on August 31, 2011; accepted on September 25, 2011 1 INTRODUCTION Transcription is the first step in the flow of biological information from genome to proteome and its tight regulation serves as a crucial To whom correspondence should be addressed. checkpoint in most biological processes. Transcriptional control often results from the concerted action of diverse transcription factors (TFs), acting alone or as interacting partners, regulating or being targeted, and participating in complex feedback loops (Lemon and Tijian, 2000; Teixeira et al., 2010). Genome-wide studies have been unveiling intricate regulatory networks with increasing layers of complexity as the hierarchy is amplified, empowered by the rapid accumulation of regulatory data in public repositories. Namely, YEASTRACT (Abdulrehman et al., 2011) contains TF–target links for Saccharomyces cerevisiae, while JASPAR (Sandelin et al., 2004) and TRANSFAC (Wingender, 1996) collect binding sites and position-specific scoring matrices for diverse eukaryotes including human. These data provide information on the topology of the regulatory network, which is static and thus not sufficient per se to determine whether a given association is relevant or not in a specific biological context. In fact, binding of a given TF to the promoter region of its target(s) is rather an intermittent event triggered by biochemical stimuli and ultimately leading to changes in expression. Insight on the mechanisms underlying the stimulus–response effect can only be achieved through an integrated study of control and behavior, where three challenges often arise: (i) identification of regulators of genes involved in a similar, related biological process; (ii) identification of genes coregulated by a group of TFs of interest; and (iii) prioritization of regulators, target genes or regulatory interactions with respect to a measure of relevance expressing their contribution within the regulatory network under study. Diverse strategies have been proposed to address the first challenge. A popular one is to rank TFs based on the ratio of genes targeted in the dataset under analysis. This score can be normalized by the relative number of targets in the genome to avoid excessive bias toward TFs controlling very large regulons (Teixeira et al., 2006). Alternatively, methods may rely on a statistical framework to discover enriched target binding sites by calculating their overrepresentation in the test sequences against a background model estimated from a collection of (randomly) selected sequences (Hestand et al., 2008; Marstrand et al., 2008; Veerla et al., 2010), eventually considering cross-species conservation (Hestand et al., 2008; Veerla et al., 2010). A drawback of such procedure is that results are highly susceptible to the choice of the background model and variations on the statistical parameters. Other strategies have overcome this limitation by computing the genome-wide overrepresentation of binding sites (Chang et al., 2006; Ho Sui et al., © The Author 2011. Published by Oxford University Press. All rights reserved. For Permissions, please email: [email protected] 3149

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INDIAN RARE EARTHS LIMITED (IREL)

INVITES

GLOBAL EXPRESSION OF INTEREST (EOI)

FOR

SETTING UP OF TITANIA SLAG PLANT

BY USING ILMENITE PRODUCED

AT

ORISSA SANDS COMPLEX (OSCOM), ODISHA, INDIA

ON

BUILD OWN OPERATE TRANSFER (BOOT) BASIS

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NOTICE INVITING EOI

Indian Rare Earths Limited (IREL), (here in after referred to as IREL) invites Global EOI

for setting up of Titania Slag Plant by using ilmenite produced at OSCOM plant located

at Chatrapur, Ganjam District, Odisha on Build, Own, Operate & Transfer (BOOT) basis

from interested bidders as detailed herein below:

Interested bidders may furnish their EOI with an approach paper and all other

necessary documents in a sealed envelope along with the covering letter duly signed by

an authorized signatory in conformity to the details furnished below:

1. EOI notice No. : IRE/CO/PT/EOI/38/2016 dated 19.09.2016

2. Type of EOI : Open (Globally)

3. Participants : Sole Bidder/Partnership/Company/LLP/Consortium

4. Name of work : 1,00,000 tons per annum (tpa) Titania Slag Plant

5. Location of work : In and around Orissa Sands Complex, Chatrapur,

Ganjam District, Odisha, India. For details refer

clause 17.2

6. Mode of work : Built-Own-Operate-Transfer (BOOT)

7. EOI Documents

Download Start Date &

Time from Website.

: : 20.09.2016 (10.00 Hrs) (IST)

8. Last Date & Time of

submission of EOI

EOI Opening

:

:

04.11.2016 (14.30 Hrs) (IST)

04.11.2016 (15.00 Hrs) (IST)

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9. Website on which EOI

notice available

: www.irel.co.in

www.tenders.gov.in

www.eprocure.gov.in

10. Address for submission

of EOI

: CGM (Technical & Corporate Planning),

Indian Rare Earths Limited,

Plot No. 1207, V.S. Marg,

ECIL Building,

Opposite Sidhivinayak Temple,

Prabhadevi, Mumbai – 400 028, India.

11. Contact Person : Name: Mr.A.Mishra

Designation: Senior Manager(Projects)

Phone No.+91 99672 68735

Email ID: [email protected]

12. Cost of EOI document : NIL

13. Earnest Money Deposit : NIL

14. Language of BID : The EOI bid prepared and submitted by the bidder

and all correspondence & documents related to the

EOI bid exchanged between the bidder and the

IREL, shall be written in English language.

Wherever such supporting documents are in

language(s) other than English, these must be

accompanied by an accurate translation of the

relevant passages which the applicant considers it

necessary to be taken into account in evaluation of

its bid by the IREL in English language. In such

case(s), for the purpose of interpretation of these

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documents, this English translation shall govern.

15. Venue & Deadline for

submission of EOI

application

: EOI bids, in its complete form in all respects as

specified in the EOI notice, shall be submitted to

IREL at the address specified above on or before the

specified due date & time of submission. IREL may,

in exceptional circumstances and at its discretion,

extend the deadline for submission of EOI bids by

issuing an addendum to be made available on the

website mentioned above.

Any amendment issued prior to due date of

submission would be put on the above mentioned

website. It would be presumed that bidders have

examined all amendments on the website and have

submitted their bids accordingly.

16. Objective of EOI

The objective of this EOI is to find out prospective bidders having expertise,

experience, resources and interest to team up with IREL and set up 1,00,000 tpa

titania slag facility under BOOT basis. The role of IREL in the tender will be as a

facilitator and enabler so that value addition of ilmenite under the drive „Make In

India‟ successful.

The concession period before transferring the plant to IREL will be for a period of

minimum ten years (extendable as per mutual consent).

The said Titania Slag Plant shall have the capacity to produce 1,00,000 tpa of

sulphatable and/or chlorinatable grade slag along with about 40,000 tpa foundry

grade pig iron (FGPI) as by product using ilmenite produced from IREL‟s plant at

OSCOM, Odisha. The specifications of ilmenite produced from OSCOM mines is

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placed at Annexure-I. The Slag Plant shall be designed with state of the art

technology.

The titania slag so produced will be the property of IREL and the same would be

taken from the BOOT operator under a long term sales purchase agreement

(SPA). The foundry grade pig iron will be the property of the BOOT operator.

17.0 About the Project:

17.1 General:

IREL is engaged in the field of heavy beach sand mining and mineral separation.

It is the largest beach sand mining and mineral separation company in India.

The total installed capacity of IREL is 5,10,000 tpa ilmenite along with other

associated minerals such as rutile, leucoxene, zircon, sillimanite and garnet etc.

As a part of value addition to ilmenite, IREL has chalked out a plant for

production of titania slag to achieve greater heights in the flow of value chain.

Titania slag plant project has been envisaged with a total capacity of 1,00,000

tpa of titania slag to be set up in or around its unit in Orissa Sands Complex,

Chatrapur, Ganjam District, Odisha, on Built-Own-Operate-Transfer (BOOT)

basis. Ilmenite produced at OSCOM shall be used as raw material for the Titania

Slag Plant.

The envisaged capacity of 1,00,000 tpa of titania slag shall be installed in two

streams of production of 50,000 tons with ore smelting furnaces in each line.

The plant shall also produce about 40,000 tpa marketable foundry grade pig iron

(FGPI).

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17.2 Location:

The proponent is to mention the tentative location of plant in the application. The

plant to be located at a place so that the logistics of raw material (ilmenite) from

Orissa Sands Complex, Matikhalo village, Chatrapur, Ganjam District, Odisha is

hassle free and also transfer of the finished product i.e. titania slag back to

IREL‟s warehouse is hassle free.

IREL may also provide necessary land within its plant premises at OSCOM to the

BOOT operator at a pre-decided lease rent. IREL shall retain the land rights.

17.3 Raw Materials and utilities:

The proposed plant will operate based on ilmenite as feedstock. Ilmenite will be

sourced from the mineral separation plant operating at Orissa Sands Complex,

Chatrpaur producing 2,20,000 tpa of ilmenite. Project for augmenting the

capacity of the OSCOM plant to produce about 4.5 lakh tpa of ilmenite and

associated minerals is in the pipe line. Thus, there is assured source of surplus

ilmenite which can be made available by IREL. Further there are huge reserves

available around coastal belt of Odisha and supply from these reserves will

ensure sufficient availability of ilmenite for the titania slag plant throughout the

year.

All the necessary utilities like water, air and electricity etc shall be arranged by

bidder. As the process is power intensive, a suitable captive power plant of

approximately 50 MW capacity may also be planned by the bidder.

17.4 Technology & Process in brief:

Ilmenite will be transported from ilmenite storage yard of OSCOM plant to the

titanium slag plant warehouse. Ilmenite with or without prior metallization will be

blended with anthracite/petroleum coke and fed into ore smelting furnace.

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The mixture will be reduced under high temperature of electric arc which will

enable ferric oxide to be converted to metallic iron and simultaneously other

metal oxide will be reduced to its metallic state. After reduction, titaniferous slag

and pig iron shall be released from furnace outlet respectively. The pig iron from

furnace outlet undergoes dephosphorization, desulphurization, carburization,

addition of inoculants and is then cast into ingots.

The titanium slag shall pass through different stages such as cooling, crushing,

magnetic separation and grinding to finally achieve the grain size required by

titania slag.

17.5 Plant Unit:

Titania slag production plant consists of the following major process unit:

Transportation, receipt and storage of raw materials i.e. ilmenite from IREL, etc.

Batching & proportioning of raw materials.

Preheating of feed materials with hot flue gases (Waste heat recovery).

Smelting reduction of the preheated charge, obtaining of conditioned titania slag

melt and co-metal in Ore Smelting Furnace.

Titania slag tapping into moulds.

Metal tapping & cooling.

Crushing, screening and magnetic separation of titania slag after hardening.

Storing and Dispatch facility of titania slag to IREL.

17.6 Consultant:

IREL may appoint a consultant to provide consultancy services for developing

the Request for Proposal (RFP) document, selection of parties and for providing

consultancy services during the stage of evaluation of the bids and for

supervision, monitoring and installation of the titania slag plant.

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17.7 Concession Period:

Ten years of plant operation & maintenance shall be considered as concession

period. IREL reserves the right to extend the concession period based on mutual

consent or decide otherwise afterwards.

18.0 Battery Limits:

Annexure-II indicates a snap shot view of the BOOT basis to be followed along

with the battery limits of IREL and the bidder.

18.1 Responsibility of IREL:

a) Land: Land shall be made available if called for to the BOOT operator at a

pre-decided lease rent. IREL shall retain the land rights.

b) Supply of ilmenite to the ilmenite warehouse of the titania slag plant.

c) Receipt of titania slag from the BOOT operator based on long term SPA

and marketing of the same.

18.2 Responsibility of BOOT Operator:

a) Receipt of ilmenite Ore from IREL‟s OSCOM Plant and other raw

materials from outside sourcing.

b) Installation of the titania slag plant & its operation.

c) Power for plant operation: bidder has to arrange the power with a suitable

captive power plant of approximately 50 MW capacity.

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d) Water required during construction stage and subsequently for operation

of Plant shall be arranged by bidder.

e) Titania Slag storage and dispatch.

19.0 Indicative Scope of work for the BOOT operator:

19.1 Conducting laboratory test work & develop flow sheets based on the feed

material i.e. OSCOM grade ilmenite and preparation of Detailed Project Report

(DPR).

19.2 Obtain various statutory clearances connected with the project.

19.3 Carry out basic engineering/detailed engineering for a plant life of minimum 20

years which inter-alia includes list of equipments with their technical

specifications, general plant layout drawings, etc.

19.4 Plant erection, installation of equipments, testing and commissioning of the plant.

19.5 Regular operation of plant.

19.6 Operation & maintenance of plant for the concession period. Successful bidder

to carry out necessary maintenance of the slag plant so as to achieve a minimum

of 95% plant availability.

19.7 Comply with the Environmental, Occupational Health & Safety and Security

requirements of IREL and has to ensure that adequate measures have been

taken from their end for the safe working of their men and machines.

19.8 Transfer of well maintained slag plant in good operating condition after replacing

all the wear & tear parts and other equipments ensuring min 95% plant

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availability in each year for last three years of the concession period to IREL or

as decided by IREL at that time.

NB:

Interested parties may contact IREL for obtaining about the details of different facilities

as mentioned above for preparation of offer at their end.

In order to understand project philosophy interested bidders are suggested to visit the

site and collect raw material samples, visit Chatrapur, Ganjam District, odisha for

obtaining information about existing facilities at OSCOM and other necessary details for

collecting preliminary data/information.

20.0 Time Schedule:

The time schedule of the above scope of the work may be considered to be 30

months (max.) from the Effective date of Contract for start of commencement of

production after installation of proposed plant.

Ten years of plant operation & maintenance shall be considered as concession

period presently. IREL reserves the right to extend the concession period,

decide otherwise afterwards. Effective date of contract shall be the date of

signing of the contract or 30 days from Letter of Acceptance, whichever is earlier.

21.0 Approach Paper to be submitted by the Prospective Bidder along with the

EOI:

The prospective bidder is required to submit an approach paper on the

methodology proposed for implementing the project, which inter-alia should

include the following details:

A) General:

a) Participating as a single entity or in the form of a consortium.

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b) In case of consortium, name of the consortium members.

c) Lead member in the consortium (It is preferred that the lead

member would be an Indian Entity).

d) Roles & Responsibilities of the consortium members.

e) Tentative share holding pattern amongst the consortium members.

f) Proposed tie-up arrangement between the consortium members at

the time of setting up & operating the plant.

g) Is any member of the consortium barred by the Government of

India/Any State Government, or any entity controlled by it, from

participating in any Bid, and if the bar subsists as on the date of

submission of the Bid.

NB: Additional information as stipulated in Annexure-III also needs to be informed.

B) Technology:

a) Name of the proposed technology partner.

b) Experience of the technology partner is operating titania slag plant

inter- alia including the following details:

i) Type of slag

ii) Capacity (tons per annum)

iii) Year of setting up of the plant:

iv) Number of years plant has operated:

v) Maximum capacity achieved by the Plant:

vi) Other by-products being produced, if any

vii) Raw material for the plant

viii) Product specifications

ix) Source of technology for the above plant i.e. whether it has

been developed in-house or technology has been sourced

c) Other details as stipulated in Annexure-IV.

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C) Financial:

a) Proposed source of finance for the project

b) Details on the financial capabilities of the consortium members to

be indicated as per the format stipulated in Annexure-V.

22.0 EOI Terms:

22.1 Pre-Bid Meeting: The pre-bid meeting will be held on 14.10.2016 at Mumbai in

order to clarify any doubts of the intending bidders. During the meeting, the

bidders are required to present techno-commercial aspects offered by them inter-

alia including parameters such as technical specifications, quality bench marks,

delivery milestones, evaluation criteria, estimates etc. Any queries to be clarified

by IREL should be submitted in writing to the following email ids at least 2 days

before the pre-bid meeting:

[email protected]

[email protected]

22.2 Request for Proposal (RFP) Terms: The bidders are required to submit salient

terms & conditions of the RFP necessary to safeguard their interest along with

the EOI documents. If found logical, IREL will include the same in the RFP to be

issued to the short-listed parties. The above details may be submitted in a

separate envelope superscribed „Proposed terms & conditions for the RFP‟.

23.0 Right to the content of the proposal:

For all the EOI bids received before the last date and time of EOI submission, the

EOI will become the property of IREL and will not be returned after opening of

the EOIs. IREL is not restricted in its rights to use or disclose any or all of the

information contained in the EOI and can do so without compensation to the

applicants. IREL shall not be bound by any language in the applications

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indicating the confidentiality of the EOI applications or any other restriction on its

use or disclosure.

24.0 Acknowledgement of Understanding of Terms

By submitting an EOI application, each applicant shall be deemed to

acknowledge that it has carefully read all sections of this EOI, including all forms,

schedules and annexure here to, and has fully informed itself as to all existing

conditions and limitations.

25.0 Submission of EOI Bid:

25.1 All pages of the EOI bid document shall be stamped & signed by the authorized

person of the firm/company/organization of applicant. Power of Attorney in

favour of signatory to EOI application shall be submitted along with the Proposal.

25.2 EOI application shall be prepared and submitted in one (1) Original and three (3)

copies in a sealed envelope superscribing “EOI for Installation of Titania Slag

Plant at OSCOM” and addressed to the following:

CGM (Technical & Corporate Planning)

Indian Rare Earths Limited,

Plot No. 1207, V.S. Marg,

ECIL Building, Opposite Sidhivinayak Temple,

Prabhadevi, Mumbai – 400 028, India.

26.0 Proposed mode of selection from shortlisted bidders:

The mode of selection will be based on the lowest responsive offer received.

Details of the same will be indicated in the RFP document.

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27.0 CHECK LIST FOR SUBMISSION OF BID (To be attached in EOI application)

S.

No.

Details of document Remarks

(Attached/Not

attached) If not

attached, reasons

1 Attachement-1: Power of Attorney

2 Attachement-2: Copies of Certificate of

Incorporation/Registration of the

Company/Partnership Deed/Affidavit for

proprietorship firm, etc.

3 Attachment-3: Copies of Profit and Loss Account

Statement for the financial years 2013-14, 2014-15

and 2015-16 in support of meeting the Financial

Eligibility Requirement.

4 Attachment-4: Copy of PAN No, if applicable.

5 Attachment-5: Salient features proposed for the RFP

6 Attachment-6: Details called for in Annexure-III to V

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Annexure I

Technical Specification of Ilmenite („OSCOM‟ Grade)

CHEMICAL ANALYSIS Qty, Mt/Yr

Guaranteed

TiO2 50.25% (Min)

Th 75 ppm (Max)

U 10 ppm (Max)

Typical:

TiO2 50.50%

FeO 34.04%

Fe2O3 12.43%

Al2O3 0.45%

SiO2 0.71%

Cr2O3 0.48%

MnO 0.51%

P2O5 0.022% V2O5 0.23%

CaO 0.04%

MgO 0.64%

Th 43ppm

U <6 ppm

SIEVE ANALYSIS

MESH (TYLER SCR.)

SIEVE OPENING MICRON

CUM. WEIGHT %RETAINE

48 300 1.7

65 212 19.7

100 150 34.3

150 106 34.5

170 90 5.4

200 75 3.7

-200 -75 0.7

Note:

1. Ilmenite being a natural product, its chemical analysis is expected to vary.

2. Variation in the size of grains, occur from time to time. Although not guaranteed, the grain

size distributions can be expected to be within the above ranges.

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Annexure-II

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Annexure-III

ADDITIONAL INFORMATION TO BE SUPPLIED BY THE BIDDER:

The following details are mandatory to be submitted by the bidder, in the following

format, failing which their offer will not be considered:

1. a) Name

b) Country of incorporation

c) Address of corporate head quarter and its branch office(s), if any in India:

d) Date of incorporation and/or commencement of business (attach copy of

MoA/ AoA or any other relevant document in this regard).

2. Brief description of the bidder including details of its main lines of business and

proposed role and responsibilities in this Project:

a) Details of Promoters/ founders

b) Current activities

3. Details of individual(s) who will serve as the point of contact/ communication for

IREL:

a) Name:

b) Designation:

c) Company:

d) Address:

e) Telephone Number:

f) E-mail Address:

g) Fax Number:

4. Particulars of the Authorized Signatory of the Applicant:

a) Name:

b) Designation:

c) Address:

d) Telephone Number:

e) Fax Number:

f) Copy of Power of Attorney to be the Authorized Signatory

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5. In case of Consortium:

a) The information above (1-4) should be provided for all the members of

the Consortium.

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Annexure-IV

S.

No.

Description Unit Achieved

(Plant in operation)

1. Specific Electrical Energy

consumption

Kwh/ tons

of TS

2. Specific consumption.

a) Petroleum coke

b) Major chemicals

tons/ tons

of TS

3. Specific Ilmenite consumption Tons of TS

4. Specific water consumption cu.m/ ton

of TS

Experience

5.

A)

Total installed capacity of the plant in

operation

tpa

B) Number of plants of minimum 25,000 tpa

capacity with same AC technology

provided by the bidder and presently in

operation

Nos.

C) Years of experience with offered

Technology.

No of

years

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Annexure-V

INFORMATION ON FINANCIAL CRITERIA

Name : …………………………………….

Values in Rs. crore

Turnover

Years Total Average

Audited

Accounts Page

Reference

Group turn

over

Capital

Employed

Net Worth

(Name & Signature of Authorized Signatory) _____________________.

Instructions:

1. For conversion of other currencies to Indian Rupees, the rate of conversion

shall be as per the Reserve Bank of India (“RBI”) reference rate as on date of

opening of the techno-commercial bid.

2. The page reference numbers indicating the financial parameters should be

indicated in the allotted column of the table and the number should be

highlighted.