ד"ר משה גולדשטיין

1982 – BSc, Computer Science, Universidad de la Republica, Uruguay.

1987 – MSc,  Computer Science, Ben-Gurion University of the Negev.

                Thesis Title: "The Design and Implementation of GISD: A Graphical Interactive  System for Conceptual Database Design".

            Supervisors: Prof. Ehud Gudes and Prof. Peretz Shoval

2010 – PhD, Computational Chemistry, The Hebrew University of Jerusalem.

            Thesis Title: "DEEPSAM (Diffusion Equation Evolutionary Programming Simulated Annealing Method) – A new Hybrid Evolutionary Algorithm for Finding the Lowest Minima of Potential Surfaces: Approach and Applications".

           Supervisor: Prof. R. Benny Gerber.

Book Sections (reviewed)

262. Fredj, M. Goldstein: "A Knowledge-Based Approach to Initial Population Generation in Evolutionary Algorithms: Application to the Protein Structure Prediction Problem". In: N. Dershowitz, E. Nissan (eds.). LNCS vol. 8001, pp. 252–262. Springer, Heidelberg, (2014).

Impact Factor:  1.17 (2018)   Scimago Rank: 0.28 (Q2)

Total Citations: 3    Non-self-Citations: 0

Peer-Reviewed Papers in Refereed Journals

• Before latest appointment

1. Shoval, E. Gudes and M. Goldstein: "GISD: A Graphical Interactive System for Conceptual Database Design", Information Systems, vol. 13 No.1, pp 81-95, (1988).

Impact Factor:  2.55 (2018)   Scimago Rank: 0.81 (Q1)   Total Citations: 9    Non-self-Citations: 9

2. Goldstein, E. Fredj, and R. B. Gerber: "A New Hybrid Algorithm for Finding the Lowest Minima of Potential Surfaces: Approach and Applications to Peptides", J. of Computational Chemistry, vol. 32, pp 1785–1800, (2011).

Impact Factor:  3.22 (2018)  Scimago Rank: 1.2 (Q1)    Total Citations: 15    Non-self-Citations: 11

3. Goldtzvik, M. Goldstein, R. B. Gerber: "On the crystallographic accuracy of structure prediction by implicit water models: Tests for cyclic peptides", Chemical Physics, vol. 415, pp. 168-172, (2013).

Impact Factor:  2.84 (2018)   Scimago Rank: 0.58 (Q2)   Total Citations: 7    Non-self-Citations: 5

4. Goldstein, L. Zmiri, E. Segev, Th. Wyttenbach, R. B. Gerber: "An atomistic structure of ubiquitin +13 relevant in mass spectrometry: Theoretical prediction and comparison with experimental cross sections", International Journal of Mass Spectrometry, vol. 367, pp. 10-15, (2014).

Impact Factor:  1.82 (2018)   Scimago Rank: 0.61 (Q2)  Total Citations: 12    Non-self-Citations: 10

• Since latest appointment

5. Amitay, M. Goldstein: "Evaluating the peptide structure prediction capabilities of a purely ab-initio method ", Protein Engineering, Design and Selection (PEDS), vol. 30, nr. 10, pp. 1-5, (2017).

Impact Factor:  1.98 (2018)   Scimago Rank: 1.02 (Q1)  Total Citations: 2    Non-self-Citations: 2

6. Aker, Sh. Ohanona, Sh. Fisher, E. Kushelevski, Sh Dvorkin, E. Kopelowitz, M. Goldstein, Z. Barnett-Itzhaki, M. Amitay: "CDB – a Database for Protein Heterodimeric Complexes", Protein Engineering, Design and Selection (PEDS), vol. 31, nr. 10, pp 361-365, (2018).

Impact Factor:  1.98 (2018)   Scimago Rank: 1.02 (Q1)   Total Citations: 0    Non-self-Citations: 0

7. Gantman, M. Goldstein, E. Segev, R. B. Gerber: "Conformers of Ubiquitin 6+ for Different Charge Distributions: Atomistic Strructures and Ion Mobility Cross Sections", The Journal of Physical Chemistry B, vol. 123, nr. 30, pp 6401-6409, (2019).

                       Impact Factor:  2.92 (2018)   Scimago Rank: 1.11 (Q1) Total Citations: 0    Non-self-Citations: 0

8. Kordic, M. Popovic, M. Popovic, M. Goldstein, M. Amitay, D. Dayan, E. Fredj: “A Computational-Chemistry Program Architecture Based on a Software Transactional Memory”, in review at Rev. Roum. Sci. Techn. – Electrotechn. Et Energ. (2020).

                        Impact Factor:  0.763 (2018/2019)   Scimago Rank: 0.22 (Q3)

Peer-Reviewed Papers in Refereed Conference Proceedings

• Before latest appointment

1. B. Yehezkael, M. Goldstein, D. Dayan, and Sh. Mizrahi: "Flexible Algorithms: Enabling Well-defined Order-Independet Execution with an Imperative Programming Style", Proc. of ECBS-EERC 2015, pp 75-82, IEEE Press, (2015).

Total Citations: 4    Non-self-Citations: 0

2. Dayan, M. Goldstein, M. Popovic, Sh. Mizrahi, M. Rabin, D. Berlovitz, O. Berlovitz, E. Bussani Levy, M. Naaman, M. Nagar, D. Soudry, R. B. Yehezkael: "EFL: Implementing and Testing an Embedded Language Which Provides Safe and Efficient Parallel Execution", Proc. of ECBS-EERC 2015, pp. 83-90, IEEE Press, (2015).

Total Citations: 3    Non-self-Citations:0

• Since latest appointment

3. Goldstein: "DEEPSAM: A Hybrid Evolutionary Algorithm for the Prediction of Biomolecules Structure", Proc. of HM2016, LNCS vol 9668, pp. 218-221, Springer, (2016).

Total Citations: 2    Non-self-Citations: 2

4. Goldstein, D. Dayan, M. Rabin, D. Berlovitz, O. Berlovitz, R. B. Yehezkael: " Design principles of an embedded language (EFL) enabling well defined order-independent execution ", Proc. of ECBS 2017, 8 pages, ACM, (2017).

Total Citations: 1    Non-self-Citations: 0

5. Eliezer, M. Goldstein: "Implementing Hammock Cost Techniques using the parallel programming paradigm of EFL (Embedded Flexible Language) ", Proc. of ZINC 2018, pp. 132-134, IEEE Press, (2018).

Total Citations: 1    Non-self-Citations: 0

6. Goldstein, A. Stulman: “Did you also fall asleep during a Principles of Programming Languages lecture? – How did a re-design of a PPL course succeed to keep the students tuned-in?”, Proc. of the InSITE 2019 conference, Jerusalem, Israel, pp. 111-117, InSITE, (2019).

https://doi.org/10.28945/4329.

Total Citations: 0    Non-self-Citations: 0

7. Kordic, M. Popovic, M. Popovic, M. Goldstein, M. Amitay, D. Dayan: “A Protein Structure Prediction Program Architecture Based on a Software Transactional Memory”, Proc. of the ECBS 2019 conference, Bucharest, Romania, 9 pages, ACM, (2019).

https://doi.org/10.1145/3352700.3352701.

Total Citations: 0    Non-self-Citations: 0 (18 downloads from the ACM DL)

Patents

"Shared Lock-Free OR-Memory for Parallel and Concurrent Systems"

Technology inventors: R. B. Yehezkael, Sh. Mizrahi, M. Goldstein, D. Dayan, D. Berlowitz, E. Lax, R. Attia. 

In date July/24^t/2018, our new OR-Memory technology was registered as a provisional patent in Israel and the USA. In date July/24/2019 it was as a patent in Israel and the USA (its approval is pending). We are trying to get investor(s), or partners, to transform our prototype into a commercial product.

In the academic years 2011-12 and 2014-15, Dr. R. B. Yehezkael, Dr. D. Dayan, Dr. Sh. Mizrahi and me, were granted JCT internal grants which allowed us to found JCT's FlexComp Research Lab and expand its activities. Those two grants allowed us to purchase two powerful HP workstations, 16 4-core Raspberry Pi cards, and the hardware components used to build the OR-memory prototype. With respect to all our research activities at Flexcomp, visit our website (flexcomp.jct.ac.il).

The results of research our work on Flexible Computation in general, and on our Embedded Flexible Language (EFL) in particular, were published in articles cited above. It is important to note here that our research related to our new OR-memory technology has not been published yet in any scientific publication because of the patent issue.

Conference Lectures (reviewed)

• Before latest appointment

1. Goldstein: "A New Algorithm for Predicting the Structure of Biological Molecules", presented at the "Biomolecular Modelling and Simulations" Safed Summer Workshop, Safed, Israel, (September 13-16, 2009).
2. Goldstein, D. Dayan, M. Popovic, D. Berlowitz, O. Berlowitz, M. Rabin, and R. B. Yehezkael: "EFL: An Embedded Language for Safe and Efficient Parallel Execution", presented at the "Intel Compiler, Architecture and Tools" Conference (CATC), Haifa, Israel, (December 1st, 2014).
3. Goldstein, D. Dayan, M. Nagar, D. Soudry, E. Bussani Levy, M. Naaman, and R. B. Yehezkael: "Implementing Parallel Programming Design Patterns Using an Embedded Flexible Language (EFL) for Python", presented at EuroPython 2016, in Bilbao, Spain, (July 17-24, 2016).
4. Amitay, M. Goldstein: " Evaluating the peptide structure prediction capabilities of a purely ab-initio method ", a short talk presented at the 82th Conference of the Israel Chemical Society, Tel-Aviv, Israel, (February 13-14, 2017).

• Since latest appointment

5. Eliezer, M. Goldstein, D. Dayan: "About the Trade-off between Time and Space Consumption when combining the Hammock-Cost Model with the EFL (Embedded Flexible Language) Parallel Programming Paradigm. ", presented at the CIVIL-COMP & CIVIL-COMP-OPTI 2019 conference, Riva del Garda, Italy, September 16-19, 2019.

Invited Seminars

• Before latest appointment

1. "DEEPSAM - A New Hybrid Algorithm for Finding the Lowest Minima of Potential Surfaces: Approach and Applications to Peptides", given at the Pasteur Institute, Montevideo, Uruguay, (September 11^th, 2011).
2. "Evaluating the peptide structure prediction capabilities of a purely ab-initio method ", given at the Dept. of Chemistry of Ben Gurion University, Beersheva, Israel (December 26^th, 2017)

Posters (reviewed)

• Before latest appointment

6. Goldstein, D. Dayan, M. Popovic, D. Berlowitz, O. Berlowitz, M. Rabin, and R. B. Yehezkael: "EFL: An Embedded Language for Safe and Efficient Parallel Execution", presented at the EuroPython 2014 Conference, Berlin, Germany, (July 21-27, 2014).
7. Goldstein, D. Dayan, D. Berlowitz, O. Berlowitz, M. Rabin, M. Nagar, D. Soudry, E. Bussani Levy, M. Naaman, R. B. Yehezkael: "Parallel Programming Constructs and Techniques using an Embedded Flexible Language (EFL) for Python", presented at the EuroPython 2015 Conference, Bilbao, Spain, (July 20-26, 2015).
8. Amitay, M. Goldstein: "Evaluating the peptide structure prediction capabilities of a purely ab-initio method", presented at the 82th Conference of the Israel Chemical Society, Tel-Aviv, Israel, (February 13-14, 2017).

Conference Organization

• Before latest appointment

1. Member of the Program Working Group of the EuroPython 2015 Conference, Bilbao, Spain, (July 20-26, 2015).
2. Member of the Program Working Group of the EuroPython 2016 Conference, Bilbao, Spain, (July 17-24, 2016).
3. Member of the Steering Committee of the ECBS 2017 Conference, Larnaca, Cyprus (August 31^st – September 1st, 2017).

• Since latest appointment

1. Member of the Steering Committee of the ECBS 2019 Conference, held at Bucharest, Romania (September 1^st – September 2^nd, 2019).
2. Member of the Steering Committee of the ECBS 2020 Conference, planned to be held at Novi Sad, Serbia (perhaps it will take place in September 2020 – all depends on the Corona crisis).

Conference Special Sessions

• Before latest appointment

1. Instructor and Organizer of the "Python Beginner's Day" session, at the EuroPython 2015 Conference, Bilbao, Spain, (July 20-26, 2015).
2. Instructor and Organizer of the "Python Beginner's Day" session, at the EuroPython 2016 Conference, Bilbao, Spain, (July 17-24, 2016).

Conference Session Chair

• Before latest appointment

1. Chairman of Session Nr. 5 of the Fritz Haber Marathon 2015, Jerusalem, Israel, (May 4-5, 2015).
2. Chairman of Session Nr. 9 ("New Frontier for Biological Systems") of The Batsheva de Rothschild Seminar on Current Challenges in Chemical Dynamics: From Exotic Novel Species to Macromolecules, Neve Ilan, Israel, (October 12-15, 2015).
3. Chairman of Oral Session Nr. 3 of HM 2016, Plymouth, UK, (June 8^th – 10^th , 2016).
4. Chairman of Software Engineering Session Nr. 3 of ECBS 2017, Larnaca, Cyprus, (August 31^st – September 1^st , 2017).

• Since latest appointment

5. Chairman of Parallel and Distributed Systems Session Nr. 2 of ECBS 2019, Bucharest, Romania, (September 2^nd – September 3^rd , 2019).

Journal and Conference Refereeing

• Before latest appointment

1. In 2012 I was the referee of a paper submitted to the journal "National Academy Science Letters", from India, published by Springer.
2. I was the referee of two papers submitted to the IcETRAN 2016 Conference, which took place in Zlatibor, Serbia (June 13-16, 2016).
3. In 2017 I was the referee of a paper submitted to the journal IEEE Transactions on Computational Biology and Bioinformatics.
4. In 2017 I was the referee of one paper submitted to the journal Physical Chemistry Chemical Physics.
5. I was the referee of two papers submitted to ECBS 2017, which took place in Larnaca, Cyprus, (August 31^st – September 1^st, 2017).

• Since latest appointment

6. I was the referee of three papers submitted to ECBS 2019, which took place in Bucharest, Romania, (September 2^nd – September 3^rd, 2019).

Courses Taught at JCT

• For Hebrew speakers
  1. Principles of File Management Systems, as lecturer, lab instructor, and course coordinator (after the approval of the new learning plan of Computer Science and Software Engineering, this course was discontinued).
  2. Principles of Database Management Systems, as lecturer and join course coordinator.
  3. Functional Programming (part of the Functional and Logic Programming course), as lecturer, course coordinator, and course designer and planner.
  4. Principles of Programming Languages, as lecturer, lab instructor, and join course coordinator.
  5. Mini-Project on File Management Systems, as instructor, course coordinator, and contents developer and planner (after the approval of the new learning plan of Computer Science and Software Engineering, this course was discontinued).
  6. Mini-Project on Database Management Systems, as course coordinator, course designer and planner.

• For English speakers
  7. Basic Business Python Programming (as instructor of a course taught in English for English speakers).
  8. Functional Programming (part of the Functional and Logic Programming course), as lecturer, course coordinator, and course designer and planner.
  9. Principles of Database Management Systems, as lecturer and course coordinator.

Courses Taught at the Hebrew University

1. Basic Python Programming for Natural Sciences.
2. Basic Python Programming for Biology.
3. Basic Python Programming for Business Administration.
4. Advanced Python Programming for Biology.
5. Python Programming for Bio-Medical Sciences.
6. SQL databases for Geography.

Public Service

1. Member of JCT's Senate Committee for the improvement of teaching at JCT (from 2010 until 2014).
2. Database Administrator (DBA) of JCT's Oracle RDBMS (from 2000 until now), serving all academic Oracle users, from all the departments at JCT.

Research and Development Activities

Summary of Past Research and Development Activities

Note: Since the beginning of my tenure here, at JCT, I have been the advisor of a lot BSc final projects. Only those done during the last years, and which are connected with my research activities, will be referred to here.

• During my PhD work (and until now) I have been developing mgTINKER, a molecular mechanics computational chemistry software package based on the world-wide used TINKER package. mgTINKER includes DEEPSAM, my PhD algorithm. DEEPSAM is an evolutionary algorithm, written in the Python programming language, as a software layer upon TINKER's Fortran77 code.
• At the Fritz Haber Research Center of the Hebrew University, using DEEPSAM, (a) the structure of relatively short cyclic peptides was predicted in vacuum and in solution, (b) the influence of implicit solvent models on protein structure prediction calculations was researched, (c) the structure of the Ubiquitin +13 protein ion, in mass spectrometric conditions, was predicted, (d) the structures of Ubiquitin +6 protein ions, in mass spectrometric conditions, were predicted, (e) the structures of several medium-size peptides and proteins, were predicted. Several papers were published about DEEPSAM and the bio-molecules’ structure prediction results obtained using it (details may be found above).
• At our FlexComp Lab at JCT, we have been researching and implementing the idea of Flexible Algorithms and Flexible Computation, as a Parallel Programming Methodology, which has been implemented at the software level as an embedded programming language called Embedded Flexible Language – EFL, and also at the hardware level as a completely new memory technology for multi-processor systems, called by us OR-memory. All this work has been done since the foundation of our Flexcomp Lab, in the 2011-12 academic year. Part of our research activities are in collaboration with European research partners from Serbia. Several papers and several posters were presented in international conferences, between 2014 and 2018 (details may be found above).
• At JCT, I was the advisor of a BSc project, in which a force field parameterization management system was developed, in two versions: (a) an offline Python application whose GUI was developed using the PyQT framework, integrated with a Python class build on top of the mgTINKER package; (b) a web-application version was developed too, to allow bio-chemistry researchers from all over the world to use our system - this web-application was developed using the Python-based Flask web-development framework. I intend to write a paper describing this two projects.
• At JCT, two research projects were done in collaboration with Dr. Amitay from JCT's Bio-Informatics Dept. In one of those projects, an in-depth test of DEEPSAM's structure prediction capabilities, in comparison with other widely used structure prediction programs, was done, A lecture (and a poster) was presented at the 82th Conference of the Israel Chemical Society in February 2017. A paper describing this research project was published in the October 2017 issue of the PEDS journal (see details above). One of the figures of this paper was selected by the editors of the PEDS journal as the cover image of the October 2017 issue; this is considered a very high academic achievement. In December 2017, I gave a seminar lecture at the Dept. of Chemistry of Ben-Gurion University, about the results of the research published in that paper. In the other project, a web-based application, called CDB, was implemented for the data management of bio-chemical complexes; two Machon Tal’s students implemented it as their final BSc project (Dr. M. Amitay and me were their advisors). A paper about this project was published in the PEDS journal in October 2018 (for details, see above).
• At our FlexComp Lab at JCT, in collaboration with Dr. R. B Yehezkael, Dr. D. Dayan (from JCT's FlexComp Lab), an instructional program, and material, was developed and written, for teaching an introductory course on Parallel and Distributed Computing and Programming, based on the idea of Flexible Algorithms and Flexible Computation. We would like to try this teaching material in a course at a High School (perhaps our ישיבה תיכונית?) or as a first year course at an academic institution (like JCT, for example).
• At our FlexComp Lab at JCT, in collaboration with Dr. R. B. Yehezkael, Dr. D. Dayan, and Dr. Sh. Mizrahi, the OR-memory technology (for which a patent was registered – see above), was developed based on the idea of Flexible Algorithms and Flexible Computation. A prototype was built as a BSc project of two graduates from JCT's Electronics Dept. This research and development achievement has not been published yet because of our intension of commercializing this technology, patented by us.
• At JCT, I was one of the advisors of the BSc final project of a student of the Bio-Informatics Dept., in which a computational biology algorithm was developed, which allows to identify the occurrence of viruses in biological samples. A paper describing this project will be prepared to be published in a Computational Biology journal.
• As coordinator of our course “Functional and Logic Programming”, I developed a new the Functional Programming part of the course, which, since the 5778 academic year, is based in a new teaching approach, using the popular programming language Python. This new approach proved to be very successful and challenging for the students.
• As coordinator of our course “Mini-project on Databases”, I developed a completely new and innovating version of the course, which, since the 5778 academic year, emphasizes team work and sub-schemata and sub-systems integration (the lab class behaves as a group of 3-member teams that work independently at the first half of the semester; later, at the second half, each team integrates/puts together sub-schemata and sub-systems that other fellow teams did during the first part). This new approach proved to be very successful and challenging for the students. During the first semester of this academic year, I started to work on the draft of a paper about the experience with this new approach of teaching/learning the subject.
• In collaboration with Prof. Miroslav Popovic’s group (my Serbian’s research partners), and my JCT’s colleagues Dr. Moshe Amitay and Dr. David Dayan, we researched the influence of using Software Transactional Memory (STM) in the running performance of DEEPSAM. A paper was presented and published at the ECBS 2019 conference, which took place in Romania in September 2019. During the first semester of this academic year, we wrote an extended version of this paper, submitted it to a journal, and after two revision iterations, it was accepted (see above).
• In collaboration with Arieh Rokach, a Mathematics and Programming teacher of the TorahUmadah high-school, we have been developing a new algorithm for computing the GCD of a set of natural number of any size. During the first semester of the current academic year, we have implemented the algorithm in two versions, one sequential and the other EFL-based (parallel). We already got very interesting preliminary results, and we continue working on this project.

Summary of Current and Future Research and Development Activities

• In collaboration with my research partner, Dr. Oren Eliezer (a lecturer at JCT’s Computer Science department), we have been researching the idea of using EFL in combination with the Hammock technique for project management. A “research in progress” paper was presented at the ZINC 2018 conference which took place in Novi Sad, Serbia, in May 2018. We presented a further development of the idea at the CIVIL-COMP & CIVIL-COMP-OPTI 2019 conference, which was held in Riva del Garda, Italy, in September 16-19, 2019. Since the beginning of the 5780 academic year we have continued our research on this idea. We are starting to see preliminary results, and we intend to publish them when we will get to some final state. We feel that the methodology that we have been developing may be an important contribution for parallel project management. This research may continue into the next academic year.
• In collaboration with my colleague Dr. Ariel Stulman, we wrote a paper about our experience teaching our course on Principles of Programming Languages. It was presented at the InSITE 2019 conference, which took place at JCT, at June 30-July 4/2019. We plan to extend what we published in this paper, using educational research methodologies, research which will be done in collaboration with our colleague Meir Komar, from JCT. This certainly is a project to the next academic year.
• In collaboration with my colleague Dr. Yosi Peretz, from JCT, we are researching the applicability of EFL for implementing an optimization algorithm that Yosi developed and published. We also would like to compare Yosi's algorithm against DEEPSAM. This also is a research in progress that I intend to continue to be involved. Also this project will continue into the next academic year.
• In collaboration with my colleague Dr. Moshe Amitay, from JCT, we continue working on our long term join research on structure prediction of biological molecules, using DEEPSAM as our structure prediction algorithm. We intend to continue working together also in the next academic year.
• My work with Arieh Rokach will continue, until we will have the results we expect, and then we intend to publish them. I think that this research collaboration also will continue in the next academic year.
• In these days, the ethical aspects of Software Engineering (and also Machine Learning) practice became an important topic in Computer Science education. People are realizing the importance of the Ethics of the Information Technologies professions, and that it is almost mandatory to educate Engineers to be aware of the Ethical influences of their profession and of the products that they design, produce, and commercialize. We don’t have any course that deals with this important subject. Then, I proposed to the chairman of our Computer Science Dept. to develop a new course about Software Engineering and Computer Science Ethics. Working on the development of such a course requires a lot of time of learning and researching the subject. I will be happy if the Committee will agree to assign me academic/research time to do it.