Formal Verification of Temporal Properties for Parametrized Concurrent Programs and Concurrent Data Structures

Los tipos de datos concurrentes son implementaciones concurrentes de las abstracciones de datos clásicas, con la diferencia de que han sido específicamente diseñados para aprovechar el gran paralelismo disponible en las modernas arquitecturas multiprocesador y multinúcleo. La correcta manipulación de los tipos de datos concurrentes resulta esencial para demostrar la completa corrección de los sistemas de software que los utilizan. Una de las mayores dificultades a la hora de diseñar y verificar tipos de datos concurrentes surge de la necesidad de tener que razonar acerca de un número arbitrario de procesos que invocan estos tipos de datos de manera concurrente. Esto requiere considerar sistemas parametrizados. En este trabajo estudiamos la verificación formal de propiedades temporales de sistemas concurrentes parametrizados, poniendo especial énfasis en programas que manipulan estructuras de datos concurrentes. La principal dificultad a la hora de razonar acerca de sistemas concurrentes parametrizados proviene de la interacción entre el gran nivel de concurrencia que éstos poseen y la necesidad de razonar al mismo tiempo acerca de la memoria dinámica. La verificación de sistemas parametrizados resulta en sí un problema desafiante debido a que requiere razonar acerca de estructuras de datos complejas que son accedidas y modificadas por un numero ilimitado de procesos que manipulan de manera simultánea el contenido de la memoria dinámica empleando métodos de sincronización poco estructurados. En este trabajo, presentamos un marco formal basado en métodos deductivos capaz de ocuparse de la verificación de propiedades de safety y liveness de sistemas concurrentes parametrizados que manejan estructuras de datos complejas. Nuestro marco formal incluye reglas de prueba y técnicas especialmente adaptadas para sistemas parametrizados, las cuales trabajan en colaboración con procedimientos de decisión especialmente diseñados para analizar complejas estructuras de datos concurrentes. Un aspecto novedoso de nuestro marco formal es que efectúa una clara diferenciación entre el análisis del flujo de control del programa y el análisis de los datos que se manejan. El flujo de control del programa se analiza utilizando reglas de prueba y técnicas de verificación deductivas especialmente diseñadas para lidiar con sistemas parametrizados. Comenzando a partir de un programa concurrente y la especificación de una propiedad temporal, nuestras técnicas deductivas son capaces de generar un conjunto finito de condiciones de verificación cuya validez implican la satisfacción de dicha especificación temporal por parte de cualquier sistema, sin importar el número de procesos que formen parte del sistema. Las condiciones de verificación generadas se corresponden con los datos manipulados. Estudiamos el diseño de procedimientos de decisión especializados capaces de lidiar con estas condiciones de verificación de manera completamente automática. Investigamos teorías decidibles capaces de describir propiedades de tipos de datos complejos que manipulan punteros, tales como implementaciones imperativas de pilas, colas, listas y skiplists. Para cada una de estas teorías presentamos un procedimiento de decisión y una implementación práctica construida sobre SMT solvers. Estos procedimientos de decisión son finalmente utilizados para verificar de manera automática las condiciones de verificación generadas por nuestras técnicas de verificación parametrizada. Para concluir, demostramos como utilizando nuestro marco formal es posible probar no solo propiedades de safety sino además de liveness en algunas versiones de protocolos de exclusión mutua y programas que manipulan estructuras de datos concurrentes. El enfoque que presentamos en este trabajo resulta ser muy general y puede ser aplicado para verificar un amplio rango de tipos de datos concurrentes similares. Abstract Concurrent data types are concurrent implementations of classical data abstractions, specifically designed to exploit the great deal of parallelism available in modern multiprocessor and multi-core architectures. The correct manipulation of concurrent data types is essential for the overall correctness of the software system built using them. A major difficulty in designing and verifying concurrent data types arises by the need to reason about any number of threads invoking the data type simultaneously, which requires considering parametrized systems. In this work we study the formal verification of temporal properties of parametrized concurrent systems, with a special focus on programs that manipulate concurrent data structures. The main difficulty to reason about concurrent parametrized systems comes from the combination of their inherently high concurrency and the manipulation of dynamic memory. This parametrized verification problem is very challenging, because it requires to reason about complex concurrent data structures being accessed and modified by threads which simultaneously manipulate the heap using unstructured synchronization methods. In this work, we present a formal framework based on deductive methods which is capable of dealing with the verification of safety and liveness properties of concurrent parametrized systems that manipulate complex data structures. Our framework includes special proof rules and techniques adapted for parametrized systems which work in collaboration with specialized decision procedures for complex data structures. A novel aspect of our framework is that it cleanly differentiates the analysis of the program control flow from the analysis of the data being manipulated. The program control flow is analyzed using deductive proof rules and verification techniques specifically designed for coping with parametrized systems. Starting from a concurrent program and a temporal specification, our techniques generate a finite collection of verification conditions whose validity entails the satisfaction of the temporal specification by any client system, in spite of the number of threads. The verification conditions correspond to the data manipulation. We study the design of specialized decision procedures to deal with these verification conditions fully automatically. We investigate decidable theories capable of describing rich properties of complex pointer based data types such as stacks, queues, lists and skiplists. For each of these theories we present a decision procedure, and its practical implementation on top of existing SMT solvers. These decision procedures are ultimately used for automatically verifying the verification conditions generated by our specialized parametrized verification techniques. Finally, we show how using our framework it is possible to prove not only safety but also liveness properties of concurrent versions of some mutual exclusion protocols and programs that manipulate concurrent data structures. The approach we present in this work is very general, and can be applied to verify a wide range of similar concurrent data types.

Gamma rhythms and beta rhythms have different synchronization properties

Experimental and modeling efforts suggest that rhythms in the CA1 region of the hippocampus that are in the beta range (12–29 Hz) have a different dynamical structure than that of gamma (30–70 Hz). We use a simplified model to show that the different rhythms employ different dynamical mechanisms to synchronize, based on different ionic currents. The beta frequency is able to synchronize over long conduction delays (corresponding to signals traveling a significant distance in the brain) that apparently cannot be tolerated by gamma rhythms. The synchronization properties are consistent with data suggesting that gamma rhythms are used for relatively local computations whereas beta rhythms are used for higher level interactions involving more distant structures.

Motor unit synchronization is reduced in anterior knee pain

Anterior knee pain (AKP) is common and has been argued to be related to poor patellofemoral joint control due to impaired coordination of the vasti muscles. However, there are conflicting data. Changes in motor unit firing may provide more definitive evidence. Synchronization of motor unit action potentials (MUAPs) in vastus medialis obliquus (VMO) and vastus lateralis (VL) may contribute to coordination in patellofemoral joint control. We hypothesized that synchronization may be reduced in AKP. Recordings of single MUAPs were made from VMO and multiunit electromyograph (EMG) recordings were made from VL. Averages of VL EMG recordings were triggered from the single MUAPs in VMO. Motor units in VL firing in association with the VMO motor units would appear as a peak in the VL EMG average. Data were compared to previous normative data. The proportion of trials in which a peak was identified in the triggered averages of VL EMG was reduced in people with AKP (38%) compared to controls (90%). Notably, although 80% of subjects had values less than controls, 20% were within normal limits. These results provide new evidence that motor unit synchronization is modified in the presence of pain and provide evidence for motor control dysfunction in AKP. Perspective: This study shows that coordination of motor units between the medial and lateral vasti muscles in people with anterior knee pain is reduced compared to people without knee pain. It confirms that motor control dysfunction is a factor in this condition and has implications for selection of rehabilitation strategies. (c) 2005 by the American Pain Society.

Motor unit synchronization between medial and lateral vasti muscles

Objective: Accurate neuromuscular control of the patellofemoral joint is important in knee joint mechanics. Strategies to coordinate the vasti muscles, such as motor unit synchronization, may simplify control of patellar tracking. This study investigated motor unit synchronization between vastus medialis (VM) and lateralis (VL). Methods: Electromyographic (EMG) recordings of single motor unit action potentials (MUAPs) were made from VM and single- and multi-unit recordings were made from VL. Synchronization was quantified from peaks in the cross-correlogram generated from single MUAP pairs in VL and VM. The proportion of motor units in VM with synchronized firing in VL was also quantified from peaks in averages of multiunit VL EMG triggered from the VM MUAP. Results: A high degree of synchronization of motor unit firing between VM and VL was identified. Results were similar for cross-correlation (similar to 45% of cases) and triggered averages (similar to 41% of cases). Conclusions: The data suggest that synchronization between VM and VL is higher than expected. Agreement between traditional cross-correlation and triggered averaging methods suggest that this new technique may provide a more clinically viable method to quantify synchronization. Significance: High synchronization between VM and VL may provide a solution to simplify control of the mechanically unstable patellofemoral joint. (c) 2005 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Effect of knee joint angle on motor unit synchronization

Activity of the vasti has been argued to vary through knee range of movement due to changes in passive support of the patellofemoral joint and the relative contribution of these muscles to knee extension. Efficient function of the knee is dependent on optimal control of the patellofemoral joint, largely through coordinated activity of the medial and lateral quadriceps. Motor unit synchronization may provide a mechanism to coordinate the activity of vastus medialis (VMO) and vastus lateralis (VL), and may be more critical in positions of reduced passive support for the patellofemoral joint (i.e., full extension). Therefore, the aim of this study was to determine whether the degree of motor unit synchronization between the vasti muscles is dependent on joint angle. Electromyographic (EMG) recordings of single motor unit action potentials (MUAPs) were made from VMO and multiunit recordings from VL during isometric contractions of the quadriceps at 0 degrees, 30 degrees, and 60 degrees of knee flexion. The degree of synchronization between motor unit firing was evaluated by identification of peaks in the rectified EMG averages of VL, triggered from MUA-Ps in VMO. The proportion of cases in which there was a significant peak in the triggered averages was calculated. There was no significant difference in the degree of synchronization between the vasti at different knee angles (p = 0.57). These data suggest that this basic coordinative mechanism between the vasti muscles is controlled consistently throughout knee range of motion, and is not augmented at specific angles where the requirement for dynamic control of stability is increased. (D 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Synchronization processes in nonlinear systems and their relation to cortical oscillatory dynamics

This thesis was focused on theoretical models of synchronization to cortical dynamics as measured by magnetoencephalography (MEG). Dynamical systems theory was used in both identifying relevant variables for brain coordination and also in devising methods for their quantification. We presented a method for studying interactions of linear and chaotic neuronal sources using MEG beamforming techniques. We showed that such sources can be accurately reconstructed in terms of their location, temporal dynamics and possible interactions. Synchronization in low-dimensional nonlinear systems was studied to explore specific correlates of functional integration and segregation. In the case of interacting dissimilar systems, relevant coordination phenomena involved generalized and phase synchronization, which were often intermittent. Spatially-extended systems were then studied. For locally-coupled dissimilar systems, as in the case of cortical columns, clustering behaviour occurred. Synchronized clusters emerged at different frequencies and their boundaries were marked through oscillation death. The macroscopic mean field revealed sharp spectral peaks at the frequencies of the clusters and broader spectral drops at their boundaries. These results question existing models of Event Related Synchronization and Desynchronization. We re-examined the concept of the steady-state evoked response following an AM stimulus. We showed that very little variability in the AM following response could be accounted by system noise. We presented a methodology for detecting local and global nonlinear interactions from MEG data in order to account for residual variability. We found crosshemispheric nonlinear interactions of ongoing cortical rhythms concurrent with the stimulus and interactions of these rhythms with the following AM responses. Finally, we hypothesized that holistic spatial stimuli would be accompanied by the emergence of clusters in primary visual cortex resulting in frequency-specific MEG oscillations. Indeed, we found different frequency distributions in induced gamma oscillations for different spatial stimuli, which was suggestive of temporal coding of these spatial stimuli. Further, we addressed the bursting character of these oscillations, which was suggestive of intermittent nonlinear dynamics. However, we did not observe the characteristic-3/2 power-law scaling in the distribution of interburst intervals. Further, this distribution was only seldom significantly different to the one obtained in surrogate data, where nonlinear structure was destroyed. In conclusion, the work presented in this thesis suggests that advances in dynamical systems theory in conjunction with developments in magnetoencephalography may facilitate a mapping between levels of description int he brain. this may potentially represent a major advancement in neuroscience.

Towards a unified understanding of event-related changes in the EEG:the Firefly model of synchronization through cross-frequency phase modulation

Although event-related potentials (ERPs) are widely used to study sensory, perceptual and cognitive processes, it remains unknown whether they are phase-locked signals superimposed upon the ongoing electroencephalogram (EEG) or result from phase-alignment of the EEG. Previous attempts to discriminate between these hypotheses have been unsuccessful but here a new test is presented based on the prediction that ERPs generated by phase-alignment will be associated with event-related changes in frequency whereas evoked-ERPs will not. Using empirical mode decomposition (EMD), which allows measurement of narrow-band changes in the EEG without predefining frequency bands, evidence was found for transient frequency slowing in recognition memory ERPs but not in simulated data derived from the evoked model. Furthermore, the timing of phase-alignment was frequency dependent with the earliest alignment occurring at high frequencies. Based on these findings, the Firefly model was developed, which proposes that both evoked and induced power changes derive from frequency-dependent phase-alignment of the ongoing EEG. Simulated data derived from the Firefly model provided a close match with empirical data and the model was able to account for i) the shape and timing of ERPs at different scalp sites, ii) the event-related desynchronization in alpha and synchronization in theta, and iii) changes in the power density spectrum from the pre-stimulus baseline to the post-stimulus period. The Firefly Model, therefore, provides not only a unifying account of event-related changes in the EEG but also a possible mechanism for cross-frequency information processing.

On the interpretation of synchronization in EEG hyperscanning studies:a cautionary note

EEG Hyperscanning is a method for studying two or more individuals simultaneously with the objective of elucidating how co-variations in their neural activity (i.e., hyperconnectivity) are influenced by their behavioral and social interactions. The aim of this study was to compare the performance of different hyper-connectivity measures using (i) simulated data, where the degree of coupling could be systematically manipulated, and (ii) individually recorded human EEG combined into pseudo-pairs of participants where no hyper-connections could exist. With simulated data we found that each of the most widely used measures of hyperconnectivity were biased and detected hyper-connections where none existed. With pseudo-pairs of human data we found spurious hyper-connections that arose because there were genuine similarities between the EEG recorded from different people independently but under the same experimental conditions. Specifically, there were systematic differences between experimental conditions in terms of the rhythmicity of the EEG that were common across participants. As any imbalance between experimental conditions in terms of stimulus presentation or movement may affect the rhythmicity of the EEG, this problem could apply in many hyperscanning contexts. Furthermore, as these spurious hyper-connections reflected real similarities between the EEGs, they were not Type-1 errors that could be overcome by some appropriate statistical control. However, some measures that have not previously been used in hyperconnectivity studies, notably the circular correlation co-efficient (CCorr), were less susceptible to detecting spurious hyper-connections of this type. The reason for this advantage in performance is discussed and the use of the CCorr as an alternative measure of hyperconnectivity is advocated. © 2013 Burgess.

Adaptive time synchronization and frequency offset estimation for CO-OFDM

We propose a robust adaptive time synchronization and frequency offset estimation method for coherent optical orthogonal frequency division multiplexing (CO-OFDM) systems by applying electrical dispersion pre-compensation (pre-EDC) to the pilot symbol. This technique effectively eliminates the timing error due to the fiber chromatic dispersion, thus increasing significantly the accuracy of the frequency offset estimation process and improving the overall system performance. In addition, a simple design of the pilot symbol is proposed for full-range frequency offset estimation. This pilot symbol can also be used to carry useful data to effectively reduce the overhead due to time synchronization by a factor of 2.

Fiscal Divergence and Business Cycle Synchronization: Irresponsibility is Idiosyncratic

Using a panel of 21 OECD countries and 40 years of annual data, we find that countries with similar government budget positions tend to have business cycles that fluctuate more closely. That is, fiscal convergence (in the form of persistently similar ratios of government surplus/deficit to GDP) is systematically associated with more synchronized business cycles. We also find evidence that reduced fiscal deficits increase business cycle synchronization. The Maastricht "convergence criteria," used to determine eligibility for EMU, encouraged fiscal convergence and deficit reduction. They may thus have indirectly moved Europe closer to an optimum currency area, by reducing countries’ abilities to create idiosyncratic fiscal shocks. Our empirical results are economically and statistically significant, and robust.

A fiskális divergencia és a konjunktúraciklusok együttmozgása - a felelőtlen fiskális politika az aszimmetrikus sokkok forrása (Fiscal divergence and business cycle synchronization: irresponsibility is idiosyncratic)

A világ 115 országának - köztük 21 OECD-tagország - 40 évnyi adatait vizsgálva, arra a következtetésre jutottunk, hogy a hasonló állami költségvetési pozíciójú országok konjunktúraciklusai között szorosabb együttmozgás mutatható ki. Azaz, a fiskális konvergenciát (amelyet a költségvetési egyenleg GDP-hez viszonyt arányának konvergenciájaként definiáltunk) összehangoltabb konjunktúraciklusokkal lehet összefüggésbe hozni. Kutatásaink során arra is találtunk bizonyítékot, hogy a kisebb mértékű költségvetési deficitek növelik a konjunktúraciklusok együttmozgását. A maastrichti konvergenciakritériumok - amelyek az európai monetáris unió követelményeinek való megfelelést hivatottak meghatározni - a fiskális konvergenciát és a költségvetési deficit csökkentését ösztönözték, s ezzel közvetett módon hozzásegítették Európát egy optimális valutaövezet létrehozásához azáltal, hogy csökkent az egyes országok lehetősége a felelőtlen fiskális politika által gerjesztett sokkhatások létrehozására. Az általunk feltárt empirikus eredmények gazdasági és statisztikai szempontból is szignifikánsak és robusztusak. _____ Using panels of 115 countries of world – including 21 OECD countries – and 40 years of annual data, the authors find that countries with similar government budget positions tend to have business cycles that fluctuate more closely. Thus fiscal convergence (in the form of persistently similar ratios of government surplus/deficit to GDP) is systemati-cally associated with more strongly synchronized business cycles. Evidence is also found that reduced fiscal deficits increase business-cycle synchronization. The Maastricht "con-vergence criteria", used to determine eligibility for EMU, encouraged fiscal convergence and deficit reduction. So they may, indirectly, have moved Europe closer to an optimum currency area, by reducing countries abilities to create idiosyncratic fiscal shocks. The empirical results of the study are economically and statistically significant, and robust.

Isotopic data of atmospheric methane from EDML and Vostok ice cores over a full glacial cycle

The response of natural CH4 sources to climate changes will be an important factor to consider as concentrations of this potent greenhouse gas continue to increase. Polar ice cores provide the means to assess this sensitivity in the past and have shown a close connection between CH4 levels and northern hemisphere temperature variability over the last glacial cycle. However, the contribution of the various CH4 sources and sinks to these changes is still a matter of debate. Contemporaneous stable CH4 isotope records in ice cores provide additional boundary conditions for assessing changes in the CH4 sources and sinks. Here we present new ice core CH4 isotope data covering the last 160,000 years, showing a clear decoupling between CH4 loading and carbon isotopic variations over most of the record. We suggest that d13CH4 variations were not dominated by a change in the source mix but rather by climate- and CO2-related ecosystem control on the isotopic composition of the methane precursor material, especially in seasonally inundated wetlands in the tropics. In contrast, relatively stable d13CH4 intervals occurred during large CH4 loading changes concurrently with past climate changes implying that most CH4 sources (most notably tropical wetlands) responded simultaneously.

Measuring, Modeling, and Forecasting Volatility and Correlations from High-Frequency Data

This dissertation contains four essays that all share a common purpose: developing new methodologies to exploit the potential of high-frequency data for the measurement, modeling and forecasting of financial assets volatility and correlations. The first two chapters provide useful tools for univariate applications while the last two chapters develop multivariate methodologies. In chapter 1, we introduce a new class of univariate volatility models named FloGARCH models. FloGARCH models provide a parsimonious joint model for low frequency returns and realized measures, and are sufficiently flexible to capture long memory as well as asymmetries related to leverage effects. We analyze the performances of the models in a realistic numerical study and on the basis of a data set composed of 65 equities. Using more than 10 years of high-frequency transactions, we document significant statistical gains related to the FloGARCH models in terms of in-sample fit, out-of-sample fit and forecasting accuracy compared to classical and Realized GARCH models. In chapter 2, using 12 years of high-frequency transactions for 55 U.S. stocks, we argue that combining low-frequency exogenous economic indicators with high-frequency financial data improves the ability of conditionally heteroskedastic models to forecast the volatility of returns, their full multi-step ahead conditional distribution and the multi-period Value-at-Risk. Using a refined version of the Realized LGARCH model allowing for time-varying intercept and implemented with realized kernels, we document that nominal corporate profits and term spreads have strong long-run predictive ability and generate accurate risk measures forecasts over long-horizon. The results are based on several loss functions and tests, including the Model Confidence Set. Chapter 3 is a joint work with David Veredas. We study the class of disentangled realized estimators for the integrated covariance matrix of Brownian semimartingales with finite activity jumps. These estimators separate correlations and volatilities. We analyze different combinations of quantile- and median-based realized volatilities, and four estimators of realized correlations with three synchronization schemes. Their finite sample properties are studied under four data generating processes, in presence, or not, of microstructure noise, and under synchronous and asynchronous trading. The main finding is that the pre-averaged version of disentangled estimators based on Gaussian ranks (for the correlations) and median deviations (for the volatilities) provide a precise, computationally efficient, and easy alternative to measure integrated covariances on the basis of noisy and asynchronous prices. Along these lines, a minimum variance portfolio application shows the superiority of this disentangled realized estimator in terms of numerous performance metrics. Chapter 4 is co-authored with Niels S. Hansen, Asger Lunde and Kasper V. Olesen, all affiliated with CREATES at Aarhus University. We propose to use the Realized Beta GARCH model to exploit the potential of high-frequency data in commodity markets. The model produces high quality forecasts of pairwise correlations between commodities which can be used to construct a composite covariance matrix. We evaluate the quality of this matrix in a portfolio context and compare it to models used in the industry. We demonstrate significant economic gains in a realistic setting including short selling constraints and transaction costs.

Nanosecond-level time synchronization of autonomous radio detector stations for extensive air showers

To exploit the full potential of radio measurements of cosmic-ray air showers at MHz frequencies, a detector timing synchronization within 1 ns is needed. Large distributed radio detector arrays such as the Auger Engineering Radio Array (AERA) rely on timing via the Global Positioning System (GPS) for the synchronization of individual detector station clocks. Unfortunately, GPS timing is expected to have an accuracy no better than about 5 ns. In practice, in particular in AERA, the GPS clocks exhibit drifts on the order of tens of ns. We developed a technique to correct for the GPS drifts, and an independent method is used to cross-check that indeed we reach a nanosecond-scale timing accuracy by this correction. First, we operate a "beacon transmitter" which emits defined sine waves detected by AERA antennas recorded within the physics data. The relative phasing of these sine waves can be used to correct for GPS clock drifts. In addition to this, we observe radio pulses emitted by commercial airplanes, the position of which we determine in real time from Automatic Dependent Surveillance Broadcasts intercepted with a software-defined radio. From the known source location and the measured arrival times of the pulses we determine relative timing offsets between radio detector stations. We demonstrate with a combined analysis that the two methods give a consistent timing calibration with an accuracy of 2 ns or better. Consequently, the beacon method alone can be used in the future to continuously determine and correct for GPS clock drifts in each individual event measured by AERA.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.