1. 5th IEEE International Conference on Digital Ecosystems and Technologies (IEEE DEST 2011), 31 May -3 June 2011, Daejeon, Korea
A Reliable Password-based User Authentication
Scheme for Web-based Human Genome Database
System
Wei-Hsin Chen Zhen-Yu Wu1, Feipei Lai1,2,3, Yin-Hsiu Chien4, Wu-
Graduate Institute of Biomedical Electronic and Liang Hwu4
1
Bioinfomatics Department of Computer Science and Information
National Taiwan University Engineering
2
Taipei, Taiwan Graduate Institute of Biomedical Electronic and
d97945014@ntu.edu.tw Bioinfomatics
3
Department of Electrical Engineering
4
Department of Medical Genetics
National Taiwan University and Hospital
Taipei, Taiwan
Abstract—With the initial completion of Human Genome Project, Taiwan University Hospital. Here physicians help to examine
the post-genomic era is coming. Although the genome map of the genetic deficiencies of patients. They use the sequence
human has been decoded, the roles that each segment of alignment tool- BLAST [3], to align the suspected DNA
sequences acts are not totally discovered. On the other hand, with sequences, investigate the causes and pathogenic mechanisms
the rapid expansion of sequence information, the issues of data of the genetic diseases.
compilation and data storage are increasingly important.
Recently, a “Web-based Human Genome Database System” is Recently, a “Web–based Human Genome Database
implemented in National Taiwan University Hospital. The System” (WHGDS) is implemented in National Taiwan
achievement of this system is that it integrates the modules of University Hospital (NTUH). The achievement of this system
sequence alignment and data compression on genome. For goals is that it integrates the modules of sequence alignment and data
of secure accessing this system over insecure networks, protocols compression. By embedding with the NCBI alignment program,
of user authentication become more important. They are able to blastall, it automatically aligns the uploaded sequences and
ensure the security of data transmission and users’ searches for the corresponding genomic positions. Besides, the
communication. In this paper, a password-based user system encodes the differences between sequences, effectively
authentication scheme, because of its convenience, efficiency, and compresses them and decreases the demand of storage spaces.
property of simplicity for human memory, is proposed for the At the same time, it offers a protected way to access the
system. personalized database. Also, users can quickly access the
interesting data by inputting the keywords of specimen number,
Keywords- Web-based Human Genome Database System; user
authentication; password; human memory.
GI and sequence position, etc.
This system provides the following two major features:
I. INTRODUCTION First, it integrates the components of NCBI BLAST tools
together with RepBase and RefSeq database, offers an auto-
The term “DNA sequencing” refers to a technique used to
aligning mechanism for those sequences uploaded by users.
determine the orders of nucleotides- adenine, guanine, cytosine,
Second, the system compresses those sequences by encoding
and thymine, in a DNA sequence. In many biological
the mismatches, which effectively decreases the demand of
applications, the composition of sequence need to be known
storage space.
because it tells what kind of genetic information that is carried.
For example, scientists investigate the sequence of DNA to As the sequence data accumulating day by day, the issues
determine whether there are functional segments such as genes, for data storage and data compilation become more and more
as well as to analyze those genes that carry genetic mutations. important. The goal of this study is to construct a secure web-
Knowledge of the DNA sequencing has become indispensable based human genome database system to help the users store
for basic biological process, as well as genetic diagnosis and and mange those sequence data.
forensic research [1]. Sanger biochemistry [2] is the primary
technique used for DNA sequencing since the early 1990s. The security issue for the WHGDS becomes a significant
concern. Speaking specifically, the most concerned security
DNA sequencing is applied for the purpose of genetic issue is how to ensure information privacy and security during
diagnosis in the Department of Medical Genetics of National transmission through the insecure networks. Relevant user
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2. 5th IEEE International Conference on Digital Ecosystems and Technologies (IEEE DEST 2011), 31 May -3 June 2011, Daejeon, Korea
authentication schemes or secret-key distribution protocols are represent the exact sequences of individual’s genome. Other
generally used to solve this kind of problem because these works such as the exploitation of single nucleotide
protocols are regarded as the primary safeguards in network polymorphism (SNP) and the analysis of variation for repeat
electronic applications [4-9]. Among these protocols, the copy-number are still in process. Knowledge of HGP with
password-based mechanism is the most widely employed these works can help the genetic diagnosis, forensic
method because of its efficiency [10]. Under such mechanism, identification and other biological research.
each user is allowed to select his password and keep in mind
without any additional assistant device for the further B. Genome Database
authentication process. The term “genome database” refers a database to store the
Unfortunately, most of these schemes are proven to be genome-associated data. They are utilized in many applications
unable to resist off-line password guessing attacks [11-15]. such as the analysis of genetic diseases, genetic finger-printing
Adversary can correctly guess the password of a specific user for criminology, and genetic genealogy. There are many public
by brute force attacks through intercepted information or self- genome databases and genome search engines through the
generated parameters. Endless possible problems are then internet. For examples, Genbank [17] incorporates DNA
presented with the hacking of the password. For example, the sequences from all available public sources, primarily through
malicious attacker may masquerade as a server to communicate the direct submission of sequence data from individual
with other users or impersonate as the user to log into a server laboratories and from large-scale sequencing projects. The
to acquire services. Therefore, we would like to propose a Ensembl [18] provides a bioinformatics framework to organize
secure and efficient password-based scheme suitable for the biology around the sequences of large genomes. It is a
WHGDS. comprehensive source of stable automatic annotation of the
human genome sequences. DDBJ (DNA Data Bank of Japan)
The rest of this paper is organized as follows. Section 2 processes and publishes the massive amounts of data submitted
introduces the web-based human genome database system in mainly by Japanese genome projects and sequencing teams.
NTUH. Section 3 illustrates the proposed password-based user It’s emphasized that the cooperation between data producing
authentication scheme. Security analyses are done in Section 4. teams and the data bank is crucial in carrying out these
Comparisons are given in Section 5, and finally, conclusions processes smoothly [19]. In this paper, a genome associated
are drawn in Section 6. database- RefSeq [20], is used to help construct the customized
human genome database system.
II. INTRODUCTION OF WEB-BASED HUMAN GENOME
DATABASE SYSTEM C. System Architecutre
A. Human Genome Project
With the rapid development of sequencing attained with
DNA sequencing technology, the research of human genome
become possible. The Human Genome Project (HGP) was an
international cooperative project with the major goal to
determine the sequences which make up the human genome
from both a physical and functional perspective. This project
began in 1990 promoted by James D. Watson at the U.S.
National Institutes of Health. An initial draft of human genome
was released in 2000. Later, a more complete one is published
in 2003, with further research still being reported. A parallel
project was performed outside of government by the Celera
Corporation [16]. As parts of the HGP, parallel sequencing was
done for other organisms such as bacterium E. coli and mouse.
These help to improve the technology for sequencing and help
the explanation of human genes. The objective of this project
can be summarized as follows [3].
Figure 1. System architecture of WHGDS
1) Identify all the genes in human genome and exploit
their functions. This system is mainly composed by five parts:
2) Determine the sequences of the 3 billion base pairs that
1) The web server: it offers the accessment for sequencing
make up the human genome.
files uploading, file management, and genomic sequence
3) Properly store these related data in databases.
management.
4) Improve tools for data analysis.
2) Sequence converter: it invokes blastall program to
5) Address the “ethical, legal, and social issues (ELSI)”
perform the alignment works for uploaded sequences against
that arise from this project.
It should be noticed that all humans have their unique the reference sequences in RefSeq database.
genomic sequence. Those sequences depicted by HGP do not 3) RefSeq and RepBase: they provide the standard human
sequences and the repetitive element sequences, respectively.
Identify applicable sponsor/s here. If no sponsors, delete this text box.
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3. 5th IEEE International Conference on Digital Ecosystems and Technologies (IEEE DEST 2011), 31 May -3 June 2011, Daejeon, Korea
4) Alignment database and genome database: The Second, the mismatch information is saved for data
alignment database contains the alignment results output by compression. The distance with the next mismatch, the
Mega BLAST (in compressed format). The genome database is mismatch type, different nucleotides are recorded and then
the combination of the sequence data if there are some parts combined together as (differential length, mismatch type,
nucleotide). There are three kinds of mismatch type- insertion,
overlapped.
deletion, replacement. It should be noted that the mismatch
5) Sequence assembler: it is responsible for the data type- deletion, has no “nucleotide” pattern behind it. The
decompression and sequence assembly process. former example is recorded as:
D. Sequence Conversion (3, Replacement, T), (4, Deletion), (5, Insertion, C), (1,
In this section, the conversion process for uploaded Insertion, G)…
sequences is introduced. The discussion is split into several
To further transform these mismatches, Fibonacci codes are
parts including sequence pre-processing, sequence aligning and
applied to encode each “differential length”, and 2 bits are
sequence post-processing. The processing flow is described as
appended to encode each “mismatch type” and
the following:
each ”nucleotide”. Fibonacci codes [20] are utilized as an
1) Sequence Preprocessing alternative to Huffman codes when the probability distribution
The uploaded sequences are in raw format and need to be of the latter is not clear. It’s simple, fast and robust to be used
converted to FASTA format to be recognized by blastall. A to encode the series of positive integers. Each integer it
sequence in FASTA begins with a single-line description, encodes is ended with “11”, which can be recognized as the
followed by lines of sequence information. The description line separator when decoding. Hence, the mentioned mismatches
begins with a greater-than (“>“) symbol in the first word. By are illustrated in Fig. 2.
the way, it is suggested that “batch search” of BLAST is more (3,Replacement,T) (4,Deletion) (5,Insertion,C) (1,Insertion,G) (587,Replacement,A)
efficient because the entire collection of reference sequences
only need to be scanned by once. For this reason, we Differential length: Fibonacci coding
concatenate the multiple sequences into a single FASTA file, Mismatch type Replacement: 00 Insertion: 01 Deletion: 10
Nucleotide A: 00 T: 01 C: 10 G: 11
one after another with no blank lines in between sequences.
2) Sequence Aligning (0011,00,01) (1011,10) (00011,01,10) (11,01,11) (00101000101011,00,00)
After the conversion of sequences by FASTA, the sequence
converter automatically invokes a program– blastall, to execute
the alignment work. blastall has some parameters that can be
00110001101110000110110110111001010001010110000
arranged to fulfill the various purposes for alignment. The
alignment algorithm- Mega BLAST is chosen. Fig. 3 shows the Figure 2. The encoded example
sequence aligning process executed by blastall. First, the
repetitive element database- RepBase is applied to mask the Fibonacci coding is simpler and faster than other entropy
human repetitive segments occurred in the uploaded sequences. coding methods such as Huffman codes or Arithmetic encoding.
This masking effectively speeds up the search process. Second, For the same purpose to be simple and fast, we use 2 bits to
the RefSeq database is provided to address the alignment work. encode each “mismatch type.” After the compression
Those uploaded sequences are aligned with the reference completed, we store them together with the data extracted from
sequences and then mapped to the corresponding genomic the XML-report (i.e. GI, template, positions, etc.) into the
positions. alignment database.
3) Sequence Postprocessing
In this stage, a XML-parser is designed to extract the E. Sequence Retrieve
interesting information in XML report, and then transmit these The alignment database stores the alignment data of
data into alignment database. Because the alignment results uploaded sequences. The users can retrieve these data to check
occupy a large amount of storage spaces, these data should be whether they are correct or not. While these data are in
further compressed. Here a compression algorithm is proposed compressed format, they need to be decompressed before
to address this issue. First, let us consider the following displayed. The retrieving procedure is stated in this section.
alignment.
a) fastcmd
C A T C T G - G A G T C G T … fastacmd is a program provided by NCBI to get the
| | | | | | | | | | interesting segments from the huge pool of sequences. At first,
the system gets the information about GI, template and
C A G C T G A G A G T - - T … positions form alignment database. Then it invokes fastacmd to
The upper part is the uploaded sequence and the lower part retrieve the corresponding segment of reference sequence
is the reference sequence. The symbol ‘|’ in the middle according to the provided information.
indicates that the upper nucleotide and lower nucleotide are
b) Sequence Assembly
matched. Therefore, the others indicate that the base pair is
mismatched between the uploaded and reference sequences. While the information about GI, template and positions are
retrieved, the mismatches data also regained. These
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4. 5th IEEE International Conference on Digital Ecosystems and Technologies (IEEE DEST 2011), 31 May -3 June 2011, Daejeon, Korea
mismatches are in compressed format and they need to be well protection against the analysis attack of smart cards so as
decompressed for further assembly. After the reference to prevent other users to catch the values.
sequence is acquired by fastacmd, those mismatches are
appended on the reference one by the way reverse to the Step 3: S returns pwi and the smart card to Ui through a
compression process. Finally, the original sequence and its secure channel.
alignment are obtained with the reference sequence. Each
sequence is retrieved by the same method and the users can B. Login Phase
choose the interesting parts for further stored to the genome When user Ui wants to log into the remote server S, he
database. firstly inserts his smart card into a terminal and then keys in his
identification IDi along with his password pwi . The smart card
F. Genome Combination will execute the following steps automatically:
Those examined sequences are picked by the users then Compute a dynamic ID for user Ui at time T. CIDi = h(pwi )
stored to genome database. The difference between alignment h(Ni y T) h(y || IDi), where T is the timestamp of Ui ’s
database and genome database is that the latter stores the computer.
jointed sequences and these sequences can be further modified
by the users, but the alignment database only stores the Send h(y || IDi), CIDi, Ni, k and T to server S through a
uploaded sequences aligned by Mega BLAST. Furthermore, common channel.
those sequences in alignment database may overlap but this
situation will not occur in genome database. C. Verification Phase
When server S receives the login request (h(y || IDi), CIDi,
III. PROPOSED AUTHENTICATION SCHEME Ni, k, T) at time T', server S does the verification as follows:
In this section, we would like to propose a password-based Check the validity of the time interval. If T* - T ΔT holds,
authentication scheme. This scheme is composed of four S accepts the login request of Ui; otherwise, the login request is
phases. They are the registration phase, the login phase, the rejected.
verification phase, and the password change phase. Below is
the detailed description of this proposal. Compute y = c – k / x.
Before describing the details of the proposal, the notation Compute h'(pwi ) = CIDi h(Ni y T) h(y || IDi).
defined and used in this scheme is shown in Table 1. Compute ID'i = Ni h(x || h(y || IDi)) h'(pwi), and then
hash the value with y to form h(y || ID'i).
TABLE I. NOTATION DEFINED AND USED IN THE SCHEME Verify whether h(y || ID'i) is equivalent to h(y || IDi). If it is,
S accepts the login request of Ui; otherwise, the login request is
U the user
rejected. Then S computes a' = h(h'(pwi ) y T').
Pw the password of user U
Send (a', T') to Ui for a mutual authentication processing.
ID the identity of user U
When user Ui receives the reply message (a', T') from
S the remote server server S at time T'', Ui does the verification as follows:
h( ) a public one-way hash function Check whether T* - T' ΔT holds. If it does, user Ui will
a bit-wise XOR operation accept the reply message and go on to the next step; otherwise,
he refuses the reply message.
A. Registration Phase
Compute a = h(h'(pwi) y T').
Suppose user Ui wants to register to a remote server S.
Then he proposes a registration request so as to get his Verify whether a is equivalent to a'. If they are equivalent,
password and his smart card from the server as follows. user Ui confirms that server S is valid.
Step 1: Ui sends his own identification IDi to S. Compute session key sk = h(h(T' y)).
Step 2: S computes Ni = h(pwi ) h(x || h(y || IDi)) IDi, D. Password Change Phase
where || is a bit concatenation operator, x is the
secret of the remote server, pwi is the password of When user Ui wants to change his password, he inserts his
Ui chosen by S, and y is a secret number selected by smart card into a terminal device. He firstly keys in his old
the remote server and stored into each registered password pwi and then follows his new password pwnew. The
user’s smart card. smart card will execute the following steps:
S generates the secret constant value c = xy + k, where k is Compute Ni* = Ni h(pwi) h(pwnew).
a value for Ui and is computed by c - xy. Step 1: Replace the original Ni with this new one, Ni*, and
S personalizes Ui’s smart card which included with the then the password is changed.
parameters [h( ), Ni, y, k]. All parameters should be provided a
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5. 5th IEEE International Conference on Digital Ecosystems and Technologies (IEEE DEST 2011), 31 May -3 June 2011, Daejeon, Korea
E. Security Analysis assuring data integrity and security during transmission.
A password-based user authentication scheme for the Safeguarding confidential data from revelation, modification,
integrated WHGDS is effective when it can assure the system’s or deletion during its transmission is the major concern in this
security in terms of password protection, data transmission, stage.
user masquerading and system spoofing. In other words, the A session key is used in our scheme to protect the
scheme can resist various malicious attacks, including stolen- confidential data from being revealed, modified, or deleted
verifier attacks, on-line and off-line password guessing attacks, during its transmission. The session key is generated via
replay attacks, and server spoofing attacks. In this section, we hashing two numbers y and T' after the verification process. All
will analyze each in details and show how the proposed scheme of the confidential data are encrypted by the session key, which
satisfies with the above-mentioned security criteria. means that without the session key, no attacker can eavesdrop,
modify, or delete the transmitting data.
F. Password Protection
Furthermore, the session key in our scheme will be invalid
Here the passwords play a very important role for each user, whenever the communication between the user and the
such as a doctor, a nurse, a patient, or a scholar, for logging integrated system server goes to the end. This means the key
into the remote server. Assuring the security of a password is will have expired its period of usage and cannot be used any
the most crucial key-point in our security analysis. Thus, we more so that it is revoked. When the user enters the system
would like to prove that our password authentication scheme again, a new session key will be generated for him to encrypt
can withstand two kinds of attacks aimed at passwords. They his information during the current communication process.
are the stolen-verifier attack, and the password guessing attack. Therefore, there will be much difficulty for anyone to calculate
The password guessing attack can further be classified into on- any of the probable previous session keys despite using all his
line and off-line attacks. known information.
Stolen-verifier attacks mean that some machinated insiders Therefore, unless the user shares his session key on purpose
of a remote server are able to steal or modify the users’ with the third party, our scheme shows the ability to achieve
legitimate passwords or update the password-verification tables the requirement of data transmission security with the help of
stored in the server’s database. This attack would not succeed the session key.
in our scheme because the password of a user is
instantaneously generated and verified by the server, who uses
H. User Masquerading Detection
its secret values c and x upon the login phase. No passwords or
verification tables have to be kept in the server’s database; While the password authentication is being processed,
therefore, the insiders would not be able to steal or modify the conspiring attackers may impersonate the identities of the
passwords. medical staff, patients, or researchers in order to pass the
authentication phase and gain the right to access the data in the
An on-line password guessing attack means that an attacker WHGDS. To prevent the disclosure of users’ privacy, protocols
continuously guesses a possible password and tries to log into a are necessary to fend off replay attacks. A replay attack is a
remote server until he is successful. In our scheme, such kind of network attack in which a valid data transmission is
attacks can be detectable. If an adversary attempts to identify repeated maliciously. This kind of attack is generally done by
the password of Ui, he is supposed to use every guessed some machinated adversary, who intercepts the data and
password to obtain the corresponding CIDi in the login phase. transmits it repeatedly. In our scheme, we employ the concept
However, the probability of guessing the correct password is of a timestamp to avoid such attacks. When server S or user Ui
only 2-k, where k is the length of the selected password. receives a message, he firstly calculates the difference between
Generally, if a guess is wrong, server S can detect easily that the current time T* and transmitted time T. And then he will
there is an adversary trying to acquire services illegally. check whether the difference is smaller than ΔT . If it is, then
Therefore, on-line password guessing attacks cannot succeed. the message is valid; otherwise, the message may be re-sent.
An off-line password guessing attack means that an attacker Therefore, the replay attack is fruitless.
can employ some intercepted information to guess the Actually, the password in our scheme is protected by the
password of a specific user by brute force attacks. Take a cryptographic hash function, and thus an attacker is unable to
glance on our scheme. The secret parameters such as x and y generate and interpret authentication messages correctly
are protected by the cryptographic hash function and are not without the knowledge of a user’s password. It is obviously
revealed to anyone; thus, this kind of attack will not work. impossible for a person in our scheme to masquerade as a
Now, assume that an adversary has obtained the following legitimate user to log into an integrated system server and
parameters (h(y || IDi), CIDi, Ni, T) in the login phase. However, acquire system services.
without y, he cannot compute h'(pwi ) = CIDi h(Ni y T)
h(y || IDi). Similarly, it is also unable for him to calculate h'(pwi ) I. Server Spoofing Detection
= Ni h(x || h(y || IDi)) ID'i without x and IDi. Therefore,
off-line password guessing attacks can be withstood. Similar to Section C, the attack by someone masquerading
as the server to cheat other users is another security concern.
An attacker may masquerade the identity of the system to carry
G. Data Transmission Security
out illegal, imperceptible authentication behavior, and
After a user logs into the system successfully, another consequently obtain the private information of some user
crucial security issue upon authentication arises, which is
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6. 5th IEEE International Conference on Digital Ecosystems and Technologies (IEEE DEST 2011), 31 May -3 June 2011, Daejeon, Korea
through the transmitted data. This is known as server spoofing environments. This authentication scheme will be realized and
attacks: someone masquerades as the server to cheat other validated soon.
users.
There is one possible way to let a conspiring attacker ACKNOWLEDGMENT
successfully spoof the other users in such schemes. When the The authors would like to acknowledge the fund from the
attacker obtains the secret values x of a remote system, he can Microsoft Corporation and the helps from their staff.
impersonate the server. In our scheme, however, the secret
values c and x are never transmitted via a common network
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