<?xml version="1.0" encoding="us-ascii" standalone="yes"?>
<!--Created by The Vintage Group, Powered by IRIS Carbon-->
<link:linkbase xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:xl="http://www.xbrl.org/2003/XLink" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:roleRef roleURI="http://www.pharmathene.com/role/Statement-UNAUDITEDCONDENSEDCONSOLIDATEDBALANCESHEETS" xlink:type="simple" xlink:href="pip-20150331.xsd#Statement-UNAUDITEDCONDENSEDCONSOLIDATEDBALANCESHEETS" />
  <link:roleRef roleURI="http://www.pharmathene.com/role/pip-uccsoo" xlink:type="simple" xlink:href="pip-20150331.xsd#pip-uccsoo" />
  <link:roleRef roleURI="http://www.pharmathene.com/role/pip-uccsocl" xlink:type="simple" xlink:href="pip-20150331.xsd#pip-uccsocl" />
  <link:roleRef roleURI="http://www.pharmathene.com/role/pip-uccsocf" xlink:type="simple" xlink:href="pip-20150331.xsd#pip-uccsocf" />
  <link:roleRef roleURI="http://www.pharmathene.com/role/pip-ftppotld" xlink:type="simple" xlink:href="pip-20150331.xsd#pip-ftppotld" />
  <link:roleRef roleURI="http://www.pharmathene.com/role/pip-fttlnoddd" xlink:type="simple" xlink:href="pip-20150331.xsd#pip-fttlnoddd" />
  <link:roleRef roleURI="http://www.pharmathene.com/role/pip-fvmsolmafvd" xlink:type="simple" xlink:href="pip-20150331.xsd#pip-fvmsolmafvd" />
  <link:roleRef roleURI="http://www.pharmathene.com/role/Disclosure-SummaryofSignificantAccountPoliciesScheduleofEarningsPerShareDetails" xlink:type="simple" xlink:href="pip-20150331.xsd#Disclosure-SummaryofSignificantAccountPoliciesScheduleofEarningsPerShareDetails" />
  <link:calculationLink xlink:type="extended" xlink:role="http://www.pharmathene.com/role/Statement-UNAUDITEDCONDENSEDCONSOLIDATEDBALANCESHEETS">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_LiabilitiesCurrent" xlink:label="us-gaap_LiabilitiesCurrent" xlink:title="us-gaap_LiabilitiesCurrent" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_RestructuringReserveCurrent" xlink:label="us-gaap_RestructuringReserveCurrent" xlink:title="us-gaap_RestructuringReserveCurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_RestructuringReserveCurrent" xlink:title="Calculation : us-gaap_LiabilitiesCurrent to us-gaap_RestructuringReserveCurrent" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_AssetsCurrent" xlink:label="us-gaap_AssetsCurrent" xlink:title="us-gaap_AssetsCurrent" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:title="us-gaap_CashAndCashEquivalentsAtCarryingValue" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:title="Calculation : us-gaap_AssetsCurrent to us-gaap_CashAndCashEquivalentsAtCarryingValue" order="1.01" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_BilledContractReceivables" xlink:label="us-gaap_BilledContractReceivables" xlink:title="us-gaap_BilledContractReceivables" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_BilledContractReceivables" xlink:title="Calculation : us-gaap_AssetsCurrent to us-gaap_BilledContractReceivables" order="1.02" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_UnbilledContractsReceivable" xlink:label="us-gaap_UnbilledContractsReceivable" xlink:title="us-gaap_UnbilledContractsReceivable" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_UnbilledContractsReceivable" xlink:title="Calculation : us-gaap_AssetsCurrent to us-gaap_UnbilledContractsReceivable" order="1.03" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:label="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:title="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:title="Calculation : us-gaap_AssetsCurrent to us-gaap_PrepaidExpenseAndOtherAssetsCurrent" order="1.04" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_Assets" xlink:label="us-gaap_Assets" xlink:title="us-gaap_Assets" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_AssetsCurrent" xlink:title="Calculation : us-gaap_Assets to us-gaap_AssetsCurrent" order="1.06" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:label="us-gaap_PropertyPlantAndEquipmentNet" xlink:title="us-gaap_PropertyPlantAndEquipmentNet" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_PropertyPlantAndEquipmentNet" xlink:title="Calculation : us-gaap_Assets to us-gaap_PropertyPlantAndEquipmentNet" order="1.07" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_OtherAssetsNoncurrent" xlink:label="us-gaap_OtherAssetsNoncurrent" xlink:title="us-gaap_OtherAssetsNoncurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_OtherAssetsNoncurrent" xlink:title="Calculation : us-gaap_Assets to us-gaap_OtherAssetsNoncurrent" order="1.08" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_Goodwill" xlink:label="us-gaap_Goodwill" xlink:title="us-gaap_Goodwill" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_Goodwill" xlink:title="Calculation : us-gaap_Assets to us-gaap_Goodwill" order="1.09" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_Liabilities" xlink:label="us-gaap_Liabilities" xlink:title="us-gaap_Liabilities" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_LiabilitiesCurrent" xlink:title="Calculation : us-gaap_Liabilities to us-gaap_LiabilitiesCurrent" order="1.14" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_OtherLiabilitiesNoncurrent" xlink:label="us-gaap_OtherLiabilitiesNoncurrent" xlink:title="us-gaap_OtherLiabilitiesNoncurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_OtherLiabilitiesNoncurrent" xlink:title="Calculation : us-gaap_Liabilities to us-gaap_OtherLiabilitiesNoncurrent" order="1.15" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_LongTermDebtNoncurrent" xlink:label="us-gaap_LongTermDebtNoncurrent" xlink:title="us-gaap_LongTermDebtNoncurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_LongTermDebtNoncurrent" xlink:title="Calculation : us-gaap_Liabilities to us-gaap_LongTermDebtNoncurrent" order="1.16" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_DerivativeLiabilitiesNoncurrent" xlink:label="us-gaap_DerivativeLiabilitiesNoncurrent" xlink:title="us-gaap_DerivativeLiabilitiesNoncurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_DerivativeLiabilitiesNoncurrent" xlink:title="Calculation : us-gaap_Liabilities to us-gaap_DerivativeLiabilitiesNoncurrent" order="1.17" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_LiabilitiesAndStockholdersEquity" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity" xlink:title="us-gaap_LiabilitiesAndStockholdersEquity" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_Liabilities" xlink:title="Calculation : us-gaap_LiabilitiesAndStockholdersEquity to us-gaap_Liabilities" order="1.18" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_StockholdersEquity" xlink:label="us-gaap_StockholdersEquity" xlink:title="us-gaap_StockholdersEquity" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_CommonStockValue" xlink:label="us-gaap_CommonStockValue" xlink:title="us-gaap_CommonStockValue" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_CommonStockValue" xlink:title="Calculation : us-gaap_StockholdersEquity to us-gaap_CommonStockValue" order="1.19" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_AdditionalPaidInCapitalCommonStock" xlink:label="us-gaap_AdditionalPaidInCapitalCommonStock" xlink:title="us-gaap_AdditionalPaidInCapitalCommonStock" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_AdditionalPaidInCapitalCommonStock" xlink:title="Calculation : us-gaap_StockholdersEquity to us-gaap_AdditionalPaidInCapitalCommonStock" order="1.2" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeLossForeignCurrencyTranslationAdjustmentNetOfTax" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeLossForeignCurrencyTranslationAdjustmentNetOfTax" xlink:title="us-gaap_AccumulatedOtherComprehensiveIncomeLossForeignCurrencyTranslationAdjustmentNetOfTax" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeLossForeignCurrencyTranslationAdjustmentNetOfTax" xlink:title="Calculation : us-gaap_StockholdersEquity to us-gaap_AccumulatedOtherComprehensiveIncomeLossForeignCurrencyTranslationAdjustmentNetOfTax" order="1.21" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit" xlink:title="us-gaap_RetainedEarningsAccumulatedDeficit" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" xlink:title="Calculation : us-gaap_StockholdersEquity to us-gaap_RetainedEarningsAccumulatedDeficit" order="1.22" weight="1" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_StockholdersEquity" xlink:title="Calculation : us-gaap_LiabilitiesAndStockholdersEquity to us-gaap_StockholdersEquity" order="1.23" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_DerivativeInstrumentsAndHedgesLiabilities" xlink:label="us-gaap_DerivativeInstrumentsAndHedgesLiabilities" xlink:title="us-gaap_DerivativeInstrumentsAndHedgesLiabilities" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_DerivativeInstrumentsAndHedgesLiabilities" xlink:title="Calculation : us-gaap_LiabilitiesCurrent to us-gaap_DerivativeInstrumentsAndHedgesLiabilities" order="2" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_AccountsPayableCurrent" xlink:label="us-gaap_AccountsPayableCurrent" xlink:title="us-gaap_AccountsPayableCurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_AccountsPayableCurrent" xlink:title="Calculation : us-gaap_LiabilitiesCurrent to us-gaap_AccountsPayableCurrent" order="3" weight="1" />
    <link:loc xlink:type="locator" xlink:href="pip-20150331.xsd#pip_AccruedExpensesAndOtherCurrentLiabilities" xlink:label="pip_AccruedExpensesAndOtherCurrentLiabilities" xlink:title="pip_AccruedExpensesAndOtherCurrentLiabilities" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="pip_AccruedExpensesAndOtherCurrentLiabilities" xlink:title="Calculation : us-gaap_LiabilitiesCurrent to pip_AccruedExpensesAndOtherCurrentLiabilities" order="4" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_LongTermDebtCurrent" xlink:label="us-gaap_LongTermDebtCurrent" xlink:title="us-gaap_LongTermDebtCurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_LongTermDebtCurrent" xlink:title="Calculation : us-gaap_LiabilitiesCurrent to us-gaap_LongTermDebtCurrent" order="5" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_OtherLiabilitiesCurrent" xlink:label="us-gaap_OtherLiabilitiesCurrent" xlink:title="us-gaap_OtherLiabilitiesCurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_OtherLiabilitiesCurrent" xlink:title="Calculation : us-gaap_LiabilitiesCurrent to us-gaap_OtherLiabilitiesCurrent" order="6" weight="1" />
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.pharmathene.com/role/pip-uccsoo">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesMinorityInterestAndIncomeLossFromEquityMethodInvestments" xlink:label="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesMinorityInterestAndIncomeLossFromEquityMethodInvestments" xlink:title="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesMinorityInterestAndIncomeLossFromEquityMethodInvestments" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_NonoperatingIncomeExpense" xlink:label="us-gaap_NonoperatingIncomeExpense" xlink:title="us-gaap_NonoperatingIncomeExpense" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesMinorityInterestAndIncomeLossFromEquityMethodInvestments" xlink:to="us-gaap_NonoperatingIncomeExpense" xlink:title="Calculation : us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesMinorityInterestAndIncomeLossFromEquityMethodInvestments to us-gaap_NonoperatingIncomeExpense" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss" xlink:title="us-gaap_NetIncomeLoss" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesMinorityInterestAndIncomeLossFromEquityMethodInvestments" xlink:title="Calculation : us-gaap_NetIncomeLoss to us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesMinorityInterestAndIncomeLossFromEquityMethodInvestments" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_InterestAndDividendIncomeOperating" xlink:label="us-gaap_InterestAndDividendIncomeOperating" xlink:title="us-gaap_InterestAndDividendIncomeOperating" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NonoperatingIncomeExpense" xlink:to="us-gaap_InterestAndDividendIncomeOperating" xlink:title="Calculation : us-gaap_NonoperatingIncomeExpense to us-gaap_InterestAndDividendIncomeOperating" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_OperatingExpenses" xlink:label="us-gaap_OperatingExpenses" xlink:title="us-gaap_OperatingExpenses" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_ResearchAndDevelopmentExpense" xlink:label="us-gaap_ResearchAndDevelopmentExpense" xlink:title="us-gaap_ResearchAndDevelopmentExpense" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingExpenses" xlink:to="us-gaap_ResearchAndDevelopmentExpense" xlink:title="Calculation : us-gaap_OperatingExpenses to us-gaap_ResearchAndDevelopmentExpense" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_OperatingIncomeLoss" xlink:label="us-gaap_OperatingIncomeLoss" xlink:title="us-gaap_OperatingIncomeLoss" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_ContractsRevenue" xlink:label="us-gaap_ContractsRevenue" xlink:title="us-gaap_ContractsRevenue" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="us-gaap_ContractsRevenue" xlink:title="Calculation : us-gaap_OperatingIncomeLoss to us-gaap_ContractsRevenue" order="1" weight="1" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesMinorityInterestAndIncomeLossFromEquityMethodInvestments" xlink:to="us-gaap_OperatingIncomeLoss" xlink:title="Calculation : us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesMinorityInterestAndIncomeLossFromEquityMethodInvestments to us-gaap_OperatingIncomeLoss" order="2" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_CurrentIncomeTaxExpenseBenefit" xlink:label="us-gaap_CurrentIncomeTaxExpenseBenefit" xlink:title="us-gaap_CurrentIncomeTaxExpenseBenefit" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_CurrentIncomeTaxExpenseBenefit" xlink:title="Calculation : us-gaap_NetIncomeLoss to us-gaap_CurrentIncomeTaxExpenseBenefit" order="2" weight="-1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_Depreciation" xlink:label="us-gaap_Depreciation" xlink:title="us-gaap_Depreciation" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingExpenses" xlink:to="us-gaap_Depreciation" xlink:title="Calculation : us-gaap_OperatingExpenses to us-gaap_Depreciation" order="2" weight="1" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="us-gaap_OperatingExpenses" xlink:title="Calculation : us-gaap_OperatingIncomeLoss to us-gaap_OperatingExpenses" order="2" weight="-1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_InterestExpense" xlink:label="us-gaap_InterestExpense" xlink:title="us-gaap_InterestExpense" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NonoperatingIncomeExpense" xlink:to="us-gaap_InterestExpense" xlink:title="Calculation : us-gaap_NonoperatingIncomeExpense to us-gaap_InterestExpense" order="3" weight="-1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_GeneralAndAdministrativeExpense" xlink:label="us-gaap_GeneralAndAdministrativeExpense" xlink:title="us-gaap_GeneralAndAdministrativeExpense" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingExpenses" xlink:to="us-gaap_GeneralAndAdministrativeExpense" xlink:title="Calculation : us-gaap_OperatingExpenses to us-gaap_GeneralAndAdministrativeExpense" order="3" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_UnrealizedGainLossOnDerivatives" xlink:label="us-gaap_UnrealizedGainLossOnDerivatives" xlink:title="us-gaap_UnrealizedGainLossOnDerivatives" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NonoperatingIncomeExpense" xlink:to="us-gaap_UnrealizedGainLossOnDerivatives" xlink:title="Calculation : us-gaap_NonoperatingIncomeExpense to us-gaap_UnrealizedGainLossOnDerivatives" order="13" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_OtherNonoperatingIncomeExpense" xlink:label="us-gaap_OtherNonoperatingIncomeExpense" xlink:title="us-gaap_OtherNonoperatingIncomeExpense" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NonoperatingIncomeExpense" xlink:to="us-gaap_OtherNonoperatingIncomeExpense" xlink:title="Calculation : us-gaap_NonoperatingIncomeExpense to us-gaap_OtherNonoperatingIncomeExpense" order="23" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_RestructuringCharges" xlink:label="us-gaap_RestructuringCharges" xlink:title="us-gaap_RestructuringCharges" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingExpenses" xlink:to="us-gaap_RestructuringCharges" xlink:title="Calculation : us-gaap_OperatingExpenses to us-gaap_RestructuringCharges" order="13" weight="1" use="optional" />
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.pharmathene.com/role/pip-uccsocl">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_ComprehensiveIncomeNetOfTax" xlink:label="us-gaap_ComprehensiveIncomeNetOfTax" xlink:title="us-gaap_ComprehensiveIncomeNetOfTax" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_OtherComprehensiveIncomeLossForeignCurrencyTransactionAndTranslationAdjustmentNetOfTax" xlink:label="us-gaap_OtherComprehensiveIncomeLossForeignCurrencyTransactionAndTranslationAdjustmentNetOfTax" xlink:title="us-gaap_OtherComprehensiveIncomeLossForeignCurrencyTransactionAndTranslationAdjustmentNetOfTax" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_ComprehensiveIncomeNetOfTax" xlink:to="us-gaap_OtherComprehensiveIncomeLossForeignCurrencyTransactionAndTranslationAdjustmentNetOfTax" xlink:title="Calculation : us-gaap_ComprehensiveIncomeNetOfTax to us-gaap_OtherComprehensiveIncomeLossForeignCurrencyTransactionAndTranslationAdjustmentNetOfTax" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss" xlink:title="us-gaap_NetIncomeLoss" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_ComprehensiveIncomeNetOfTax" xlink:to="us-gaap_NetIncomeLoss" xlink:title="Calculation : us-gaap_ComprehensiveIncomeNetOfTax to us-gaap_NetIncomeLoss" order="2" weight="1" />
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.pharmathene.com/role/pip-uccsocf">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:label="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:title="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_EffectOfExchangeRateOnCashAndCashEquivalents" xlink:label="us-gaap_EffectOfExchangeRateOnCashAndCashEquivalents" xlink:title="us-gaap_EffectOfExchangeRateOnCashAndCashEquivalents" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:to="us-gaap_EffectOfExchangeRateOnCashAndCashEquivalents" xlink:title="Calculation : us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease to us-gaap_EffectOfExchangeRateOnCashAndCashEquivalents" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:title="us-gaap_NetCashProvidedByUsedInInvestingActivities" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment" xlink:label="us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment" xlink:title="us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInInvestingActivities to us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:title="us-gaap_NetCashProvidedByUsedInFinancingActivities" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_ProceedsFromRepaymentsOfOtherLongTermDebt" xlink:label="us-gaap_ProceedsFromRepaymentsOfOtherLongTermDebt" xlink:title="us-gaap_ProceedsFromRepaymentsOfOtherLongTermDebt" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_ProceedsFromRepaymentsOfOtherLongTermDebt" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInFinancingActivities to us-gaap_ProceedsFromRepaymentsOfOtherLongTermDebt" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:title="us-gaap_NetCashProvidedByUsedInOperatingActivities" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_IncreaseDecreaseInAccruedLiabilitiesAndOtherOperatingLiabilities" xlink:label="us-gaap_IncreaseDecreaseInAccruedLiabilitiesAndOtherOperatingLiabilities" xlink:title="us-gaap_IncreaseDecreaseInAccruedLiabilitiesAndOtherOperatingLiabilities" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInAccruedLiabilitiesAndOtherOperatingLiabilities" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_IncreaseDecreaseInAccruedLiabilitiesAndOtherOperatingLiabilities" order="1" weight="1" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:title="Calculation : us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease to us-gaap_NetCashProvidedByUsedInFinancingActivities" order="2" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:label="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:title="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInInvestingActivities to us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" order="2" weight="-1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:label="us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:title="us-gaap_ProceedsFromIssuanceOfCommonStock" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInFinancingActivities to us-gaap_ProceedsFromIssuanceOfCommonStock" order="2" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_DeferredIncomeTaxExpenseBenefit" xlink:label="us-gaap_DeferredIncomeTaxExpenseBenefit" xlink:title="us-gaap_DeferredIncomeTaxExpenseBenefit" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_DeferredIncomeTaxExpenseBenefit" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_DeferredIncomeTaxExpenseBenefit" order="2" weight="1" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:title="Calculation : us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease to us-gaap_NetCashProvidedByUsedInInvestingActivities" order="3" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_ProceedsFromRepaymentsOfLinesOfCredit" xlink:label="us-gaap_ProceedsFromRepaymentsOfLinesOfCredit" xlink:title="us-gaap_ProceedsFromRepaymentsOfLinesOfCredit" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_ProceedsFromRepaymentsOfLinesOfCredit" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInFinancingActivities to us-gaap_ProceedsFromRepaymentsOfLinesOfCredit" order="3" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_Depreciation" xlink:label="us-gaap_Depreciation" xlink:title="us-gaap_Depreciation" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_Depreciation" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_Depreciation" order="3" weight="1" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:title="Calculation : us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease to us-gaap_NetCashProvidedByUsedInOperatingActivities" order="4" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_IncreaseDecreaseInDeferredRevenue" xlink:label="us-gaap_IncreaseDecreaseInDeferredRevenue" xlink:title="us-gaap_IncreaseDecreaseInDeferredRevenue" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInDeferredRevenue" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_IncreaseDecreaseInDeferredRevenue" order="4" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_ProceedsFromWarrantExercises" xlink:label="us-gaap_ProceedsFromWarrantExercises" xlink:title="us-gaap_ProceedsFromWarrantExercises" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_ProceedsFromWarrantExercises" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInFinancingActivities to us-gaap_ProceedsFromWarrantExercises" order="4" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_IncreaseDecreaseInAccountsPayable" xlink:label="us-gaap_IncreaseDecreaseInAccountsPayable" xlink:title="us-gaap_IncreaseDecreaseInAccountsPayable" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInAccountsPayable" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_IncreaseDecreaseInAccountsPayable" order="5" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_PaymentsOfFinancingCosts" xlink:label="us-gaap_PaymentsOfFinancingCosts" xlink:title="us-gaap_PaymentsOfFinancingCosts" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_PaymentsOfFinancingCosts" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInFinancingActivities to us-gaap_PaymentsOfFinancingCosts" order="5" weight="-1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:label="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:title="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" order="6" weight="-1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_IncreaseDecreaseInUnbilledReceivables" xlink:label="us-gaap_IncreaseDecreaseInUnbilledReceivables" xlink:title="us-gaap_IncreaseDecreaseInUnbilledReceivables" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInUnbilledReceivables" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_IncreaseDecreaseInUnbilledReceivables" order="7" weight="-1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_IncreaseDecreaseInAccountsReceivable" xlink:label="us-gaap_IncreaseDecreaseInAccountsReceivable" xlink:title="us-gaap_IncreaseDecreaseInAccountsReceivable" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInAccountsReceivable" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_IncreaseDecreaseInAccountsReceivable" order="8" weight="-1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_PaidInKindInterest" xlink:label="us-gaap_PaidInKindInterest" xlink:title="us-gaap_PaidInKindInterest" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_PaidInKindInterest" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_PaidInKindInterest" order="9" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:label="us-gaap_ShareBasedCompensation" xlink:title="us-gaap_ShareBasedCompensation" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_ShareBasedCompensation" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_ShareBasedCompensation" order="10" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_GainLossOnSaleOfPropertyPlantEquipment" xlink:label="us-gaap_GainLossOnSaleOfPropertyPlantEquipment" xlink:title="us-gaap_GainLossOnSaleOfPropertyPlantEquipment" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_GainLossOnSaleOfPropertyPlantEquipment" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_GainLossOnSaleOfPropertyPlantEquipment" order="11" weight="-1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_UnrealizedGainLossOnDerivatives" xlink:label="us-gaap_UnrealizedGainLossOnDerivatives" xlink:title="us-gaap_UnrealizedGainLossOnDerivatives" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_UnrealizedGainLossOnDerivatives" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_UnrealizedGainLossOnDerivatives" order="12" weight="-1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss" xlink:title="us-gaap_NetIncomeLoss" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_NetIncomeLoss" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_NetIncomeLoss" order="13" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_RestructuringReservePeriodIncreaseDecrease" xlink:label="us-gaap_RestructuringReservePeriodIncreaseDecrease" xlink:title="us-gaap_RestructuringReservePeriodIncreaseDecrease" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_RestructuringReservePeriodIncreaseDecrease" xlink:title="Calculation : us-gaap_NetCashProvidedByUsedInOperatingActivities to us-gaap_RestructuringReservePeriodIncreaseDecrease" order="23" weight="1" use="optional" />
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.pharmathene.com/role/pip-ftppotld">
    <link:loc xlink:type="locator" xlink:href="pip-20150331.xsd#pip_LongTermDebtExcludingDiscount" xlink:label="pip_LongTermDebtExcludingDiscount" xlink:title="pip_LongTermDebtExcludingDiscount" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalRemainderOfFiscalYear" xlink:label="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalRemainderOfFiscalYear" xlink:title="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalRemainderOfFiscalYear" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="pip_LongTermDebtExcludingDiscount" xlink:to="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalRemainderOfFiscalYear" xlink:title="Calculation : pip_LongTermDebtExcludingDiscount to us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalRemainderOfFiscalYear" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalInYearTwo" xlink:label="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalInYearTwo" xlink:title="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalInYearTwo" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="pip_LongTermDebtExcludingDiscount" xlink:to="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalInYearTwo" xlink:title="Calculation : pip_LongTermDebtExcludingDiscount to us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalInYearTwo" order="2" weight="1" />
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.pharmathene.com/role/pip-fttlnoddd">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_LongTermDebt" xlink:label="us-gaap_LongTermDebt" xlink:title="us-gaap_LongTermDebt" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_LongTermDebtCurrent" xlink:label="us-gaap_LongTermDebtCurrent" xlink:title="us-gaap_LongTermDebtCurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LongTermDebt" xlink:to="us-gaap_LongTermDebtCurrent" xlink:title="Calculation : us-gaap_LongTermDebt to us-gaap_LongTermDebtCurrent" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_LongTermDebtNoncurrent" xlink:label="us-gaap_LongTermDebtNoncurrent" xlink:title="us-gaap_LongTermDebtNoncurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LongTermDebt" xlink:to="us-gaap_LongTermDebtNoncurrent" xlink:title="Calculation : us-gaap_LongTermDebt to us-gaap_LongTermDebtNoncurrent" order="2" weight="1" />
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.pharmathene.com/role/pip-fvmsolmafvd">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_DerivativeAssets" xlink:label="us-gaap_DerivativeAssets" xlink:title="us-gaap_DerivativeAssets" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_InvestmentsFairValueDisclosure" xlink:label="us-gaap_InvestmentsFairValueDisclosure" xlink:title="us-gaap_InvestmentsFairValueDisclosure" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DerivativeAssets" xlink:to="us-gaap_InvestmentsFairValueDisclosure" xlink:title="Calculation : us-gaap_DerivativeAssets to us-gaap_InvestmentsFairValueDisclosure" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_DerivativeLiabilities" xlink:label="us-gaap_DerivativeLiabilities" xlink:title="us-gaap_DerivativeLiabilities" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_DerivativeLiabilitiesCurrent" xlink:label="us-gaap_DerivativeLiabilitiesCurrent" xlink:title="us-gaap_DerivativeLiabilitiesCurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DerivativeLiabilities" xlink:to="us-gaap_DerivativeLiabilitiesCurrent" xlink:title="Calculation : us-gaap_DerivativeLiabilities to us-gaap_DerivativeLiabilitiesCurrent" order="1" weight="1" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_DerivativeLiabilitiesNoncurrent" xlink:label="us-gaap_DerivativeLiabilitiesNoncurrent" xlink:title="us-gaap_DerivativeLiabilitiesNoncurrent" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DerivativeLiabilities" xlink:to="us-gaap_DerivativeLiabilitiesNoncurrent" xlink:title="Calculation : us-gaap_DerivativeLiabilities to us-gaap_DerivativeLiabilitiesNoncurrent" order="2" weight="1" />
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.pharmathene.com/role/Disclosure-SummaryofSignificantAccountPoliciesScheduleofEarningsPerShareDetails">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" xlink:label="us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" xlink:title="us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss" xlink:title="us-gaap_NetIncomeLoss" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" xlink:to="us-gaap_NetIncomeLoss" xlink:title="Calculation : us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic to us-gaap_NetIncomeLoss" order="10" weight="1" use="optional" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_UndistributedEarningsLossAllocatedToParticipatingSecuritiesBasic" xlink:label="us-gaap_UndistributedEarningsLossAllocatedToParticipatingSecuritiesBasic" xlink:title="us-gaap_UndistributedEarningsLossAllocatedToParticipatingSecuritiesBasic" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" xlink:to="us-gaap_UndistributedEarningsLossAllocatedToParticipatingSecuritiesBasic" xlink:title="Calculation : us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic to us-gaap_UndistributedEarningsLossAllocatedToParticipatingSecuritiesBasic" order="20" weight="-1" use="optional" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted" xlink:label="us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted" xlink:title="us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted" xlink:to="us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" xlink:title="Calculation : us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted to us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" order="10" weight="1" use="optional" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_UndistributedEarningsLossAllocatedToParticipatingSecuritiesDiluted" xlink:label="us-gaap_UndistributedEarningsLossAllocatedToParticipatingSecuritiesDiluted" xlink:title="us-gaap_UndistributedEarningsLossAllocatedToParticipatingSecuritiesDiluted" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted" xlink:to="us-gaap_UndistributedEarningsLossAllocatedToParticipatingSecuritiesDiluted" xlink:title="Calculation : us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted to us-gaap_UndistributedEarningsLossAllocatedToParticipatingSecuritiesDiluted" order="20" weight="-1" use="optional" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2014/elts/us-gaap-2014-01-31.xsd#us-gaap_DilutiveSecurities" xlink:label="us-gaap_DilutiveSecurities" xlink:title="us-gaap_DilutiveSecurities" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted" xlink:to="us-gaap_DilutiveSecurities" xlink:title="Calculation : us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted to us-gaap_DilutiveSecurities" order="30" weight="1" use="optional" />
  </link:calculationLink>
</link:linkbase>
